diff --git a/common.mk b/common.mk
index 5c1f2461d1..0868088b3c 100644
--- a/common.mk
+++ b/common.mk
@@ -231,36 +231,24 @@ $(SFC_MFC_TARGETS) &: $(FIRRTL_FILE) $(FINAL_ANNO_FILE) $(SFC_LEVEL) $(EXTRA_FIR
 	$(SED) -i 's/.*/& /' $(MFC_SMEMS_CONF) # need trailing space for SFC macrocompiler
 # DOC include end: FirrtlCompiler
 
-$(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(ALL_MODS_FILELIST) $(BB_MODS_FILELIST) $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED) &: $(MFC_MODEL_HRCHY_JSON) $(MFC_FILELIST) $(MFC_BB_MODS_FILELIST)
-	$(base_dir)/scripts/split-module-files.py \
+$(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(ALL_MODS_FILELIST) $(BB_MODS_FILELIST) $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED) &: $(MFC_MODEL_HRCHY_JSON) $(MFC_TOP_HRCHY_JSON) $(MFC_FILELIST) $(MFC_BB_MODS_FILELIST)
+	$(base_dir)/scripts/uniquify-module-names.py \
 		--model-hier-json $(MFC_MODEL_HRCHY_JSON) \
+		--top-hier-json $(MFC_TOP_HRCHY_JSON) \
+		--in-all-filelist $(MFC_FILELIST) \
 		--dut $(TOP) \
+		--model $(MODEL) \
+		--target-dir $(GEN_COLLATERAL_DIR) \
 		--out-dut-filelist $(TOP_MODS_FILELIST) \
 		--out-model-filelist $(MODEL_MODS_FILELIST) \
-		--in-all-filelist $(MFC_FILELIST) \
-		--target-dir $(GEN_COLLATERAL_DIR)
+		--out-model-hier-json $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED) \
+		--gcpath $(GEN_COLLATERAL_DIR)
 	$(SED) -e 's;^;$(GEN_COLLATERAL_DIR)/;' $(MFC_BB_MODS_FILELIST) > $(BB_MODS_FILELIST)
 	$(SED) -i 's/\.\///' $(TOP_MODS_FILELIST)
 	$(SED) -i 's/\.\///' $(MODEL_MODS_FILELIST)
 	$(SED) -i 's/\.\///' $(BB_MODS_FILELIST)
-	$(base_dir)/scripts/uniqify-module-names.py \
-		--top-filelist $(TOP_MODS_FILELIST) \
-		--mod-filelist $(MODEL_MODS_FILELIST) \
-		--gen-collateral-path $(GEN_COLLATERAL_DIR) \
-		--model-hier-json $(MFC_MODEL_HRCHY_JSON) \
-		--out-model-hier-json $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED) \
-		--dut $(TOP) \
-		--model $(MODEL)
 	sort -u $(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(BB_MODS_FILELIST) > $(ALL_MODS_FILELIST)
 
-$(TOP_BB_MODS_FILELIST) $(MODEL_BB_MODS_FILELIST) &: $(BB_MODS_FILELIST) $(MFC_TOP_HRCHY_JSON) $(FINAL_ANNO_FILE)
-	$(base_dir)/scripts/split-bb-files.py \
-		--in-bb-f $(BB_MODS_FILELIST) \
-		--in-top-hrchy-json $(MFC_TOP_HRCHY_JSON) \
-		--in-anno-json $(FINAL_ANNO_FILE) \
-		--out-top-bb-f $(TOP_BB_MODS_FILELIST) \
-		--out-model-bb-f $(MODEL_BB_MODS_FILELIST)
-
 $(TOP_SMEMS_CONF) $(MODEL_SMEMS_CONF) &:  $(MFC_SMEMS_CONF) $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED)
 	$(base_dir)/scripts/split-mems-conf.py \
 		--in-smems-conf $(MFC_SMEMS_CONF) \
@@ -284,7 +272,7 @@ $(MODEL_SMEMS_FILE) $(MODEL_SMEMS_FIR) &: $(MODEL_SMEMS_CONF) | $(TOP_SMEMS_FILE
 # note: {MODEL,TOP}_BB_MODS_FILELIST is added as a req. so that the files get generated,
 #       however it is really unneeded since ALL_MODS_FILELIST includes all BB files
 ########################################################################################
-$(sim_common_files): $(sim_files) $(ALL_MODS_FILELIST) $(TOP_SMEMS_FILE) $(MODEL_SMEMS_FILE) $(TOP_BB_MODS_FILELIST) $(MODEL_BB_MODS_FILELIST)
+$(sim_common_files): $(sim_files) $(ALL_MODS_FILELIST) $(TOP_SMEMS_FILE) $(MODEL_SMEMS_FILE) $(BB_MODS_FILELIST)
 	sort -u $(sim_files) $(ALL_MODS_FILELIST) | grep -v '.*\.\(svh\|h\)$$' > $@
 	echo "$(TOP_SMEMS_FILE)" >> $@
 	echo "$(MODEL_SMEMS_FILE)" >> $@
diff --git a/scripts/split-bb-files.py b/scripts/split-bb-files.py
deleted file mode 100755
index 959a10a2e5..0000000000
--- a/scripts/split-bb-files.py
+++ /dev/null
@@ -1,82 +0,0 @@
-#!/usr/bin/env python3
-
-import json
-import argparse
-from collections import defaultdict
-
-# Schema of *.f emitted by circt
-"""
-<gen-src-dir>/<long-name>/gen-collateral/SimUART.cc
-<gen-src-dir>/<long-name>/gen-collateral/AsyncQueueSource.sv
-<gen-src-dir>/<long-name>/gen-collateral/AsyncQueueSink.sv
-<gen-src-dir>/<long-name>/gen-collateral/AsyncQueueSource_1.sv
-<gen-src-dir>/<long-name>/gen-collateral/AsyncQueueSink_1.sv
-<gen-src-dir>/<long-name>/gen-collateral/AsyncQueueSource_2.sv
-<gen-src-dir>/<long-name>/gen-collateral/AsyncQueueSink_2.sv
-<gen-src-dir>/<long-name>/gen-collateral/AsyncResetSynchronizerShiftReg_w4_d3_i0.sv
-"""
-
-def bfs_collect_submodules(tree):
-  output = set()
-  q = [(tree['instance_name'], tree['module_name'], tree['instances'])]
-
-  while len(q) != 0:
-    front = q[0]
-    q.pop(0)
-
-    (inst, mod, child) = front
-    output.add(mod)
-    for c in child:
-      q.append((c['instance_name'], c['module_name'], c['instances']))
-  return output
-
-def write_lines_to_file(lines, file_path):
-  with open(file_path, "w") as fp:
-    for line in lines:
-      fp.write("%s\n" % line)
-
-if __name__ == "__main__":
-  parser = argparse.ArgumentParser(description='Create *.model.bb.f and *.top.bb.f blackbox filelists')
-  parser.add_argument('--in-bb-f', type=str, required=True, help='All blackbox files filelist (includes both MODEL/TOP files)')
-  parser.add_argument('--in-top-hrchy-json', type=str, required=True, help='List containing hierarchy of top modules (top-module-hierarchy.json)')
-  parser.add_argument('--in-anno-json', type=str, required=True, help='Anno. file with blackbox annotations')
-  parser.add_argument('--out-top-bb-f', type=str, required=True, help='List of blackbox files for TOP')
-  parser.add_argument('--out-model-bb-f', type=str, required=True, help='List of blackbox files for MODEL')
-  args = parser.parse_args()
-
-  # module_path -> list of bb paths (not fully resolved paths)
-  mod_bb_dict = defaultdict(list)
-  with open(args.in_anno_json, "r") as f:
-    anno_data = json.load(f)
-    for anno in anno_data:
-      if 'BlackBoxInlineAnno' in anno['class']:
-        mod_bb_dict[anno['target']].append(anno['name'])
-      if 'BlackBoxPathAnno' in anno['class']:
-        mod_bb_dict[anno['target']].append(anno['path'])
-
-  with open(args.in_top_hrchy_json) as ihj:
-    ihj_data = json.load(ihj)
-    top_inner_modules = bfs_collect_submodules(ihj_data)
-
-    with open(args.in_bb_f) as ibf:
-      lines = ibf.read().splitlines()
-
-      tbfs = set()
-      for mod_path, bb_files in mod_bb_dict.items():
-        leaf_mod = mod_path.split('.')[-1]
-
-        # if matched, add the fully resolved path to the top bb filelist
-        if leaf_mod in top_inner_modules:
-          for line in lines:
-            for bb_file in bb_files:
-              if bb_file in line:
-                tbfs.add(line)
-
-      # now tbfs should be complete (need to remove tbf files from original bb file for model bb)
-      mbfs = set()
-      for line in lines:
-        if not line in tbfs:
-          mbfs.add(line)
-
-      write_lines_to_file(tbfs, args.out_top_bb_f)
-      write_lines_to_file(mbfs, args.out_model_bb_f)
diff --git a/scripts/split-module-files.py b/scripts/split-module-files.py
deleted file mode 100755
index 64fe570704..0000000000
--- a/scripts/split-module-files.py
+++ /dev/null
@@ -1,111 +0,0 @@
-#!/usr/bin/env python3
-
-import json
-import argparse
-from typing import List, Optional
-
-# Schema of json emitted by circt
-"""
-{
-  "instance_name": "TestHarness",
-  "module_name": "TestHarness",
-  "instances": [
-    {
-      "instance_name": "chiptop",
-      "module_name": "ChipTop",
-      "instances": [
-        {
-          "instance_name": "system",
-          "module_name": "DigitalTop",
-          "instances": [ ]
-        }, ...
-      ]
-    },
-    {
-      "instance_name": "simdram",
-      "module_name": "SimDRAM",
-      "instances": []
-    },
-  ]
-}
-"""
-
-def get_modules(js: dict) -> List[str]:
-    if 'instances' not in js:
-        return js['module_name']
-    else:
-        mods = []
-        for mod in js['instances']:
-            mods.extend(get_modules(mod))
-        return [js['module_name']] + mods
-
-def find_mod_by_name(js: dict, name: str) -> Optional[List[dict]]:
-    if 'instances' not in js:
-        return None
-    else:
-        mods = []
-        for mod in js['instances']:
-            if mod['module_name'] == name:
-                mods.append(mod)
-            other_mods = find_mod_by_name(mod, name)
-            if other_mods is not None:
-                mods.extend(other_mods)
-        return mods
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description='Convert CIRCT (firtool) hierarchy JSON into DUT and test harness filelists')
-    parser.add_argument('--model-hier-json', type=str, required=True, help='Path to hierarchy JSON emitted by firtool. Must include DUT as a module.')
-    parser.add_argument('--dut', type=str, required=True, help='Name of the DUT module.')
-    parser.add_argument('--out-dut-filelist', type=str, required=True, help='Path to output filelist including all modules under the DUT.')
-    parser.add_argument('--out-model-filelist', type=str, required=True, help='Path to output filelist including all modules under the top-most module but not modules under the DUT.')
-    parser.add_argument('--in-all-filelist', type=str, required=True, help='Path to input filelist that has all modules (relative paths).')
-    parser.add_argument('--target-dir', type=str, required=True, help='Path to where module sources are located (combined with --in-all-filelist gives the absolute path to module sources).')
-    args = parser.parse_args()
-
-    with open(args.model_hier_json) as f:
-        j = json.load(f)
-
-        dut_tops = find_mod_by_name(j, args.dut)
-        assert dut_tops is not None
-        assert len(dut_tops) == 1
-        dut_top = dut_tops[0]
-
-        dut_mods = set(get_modules(dut_top))
-        model_mods = set(get_modules(j)) - dut_mods
-        both_mods = dut_mods.intersection(model_mods)
-
-        assert len(both_mods) == 0
-
-        with open(args.out_dut_filelist, 'w') as df, \
-             open(args.in_all_filelist) as fl:
-            # add paths that correspond to modules to output file
-            for path in fl:
-                writeOut = False
-                for dm in dut_mods:
-                    if dm in path:
-                        writeOut = True
-                        break
-
-                # prepend the target directory to get filelist with absolute paths
-                if writeOut:
-                    if not args.target_dir in path:
-                        df.write(f"{args.target_dir}/{path}")
-                    else:
-                        df.write(f"{path}")
-
-        with open(args.out_model_filelist, 'w') as df, \
-             open(args.in_all_filelist) as fl:
-            # add paths that correspond to modules to output file
-            for path in fl:
-                writeOut = False
-                for dm in model_mods:
-                    if dm in path:
-                        writeOut = True
-                        break
-
-                # prepend the target directory to get filelist with absolute paths
-                if writeOut:
-                    if not args.target_dir in path:
-                        df.write(f"{args.target_dir}/{path}")
-                    else:
-                        df.write(f"{path}")
diff --git a/scripts/uniqify-module-names.py b/scripts/uniqify-module-names.py
deleted file mode 100755
index a6255a8c90..0000000000
--- a/scripts/uniqify-module-names.py
+++ /dev/null
@@ -1,100 +0,0 @@
-#!/usr/bin/env python3
-
-import json
-import argparse
-import shutil
-import os
-import datetime
-
-
-parser = argparse.ArgumentParser(description="")
-parser.add_argument("--top-filelist", type=str, required=True, help="Abs path to <top>.<model>.top.f")
-parser.add_argument("--mod-filelist", type=str, required=True, help="Abs path to <top>.<model>.model.f")
-parser.add_argument("--gen-collateral-path", dest="gcpath", type=str, required=True, help="Abs path to the gen-collateral directory")
-parser.add_argument("--model-hier-json", type=str, required=True, help="Path to hierarchy JSON emitted by firtool. Must include DUT as a module.")
-parser.add_argument("--out-model-hier-json", type=str, required=True, help="Path to updated hierarchy JSON emitted by this script.")
-parser.add_argument("--dut", type=str, required=True, help="Name of the DUT module.")
-parser.add_argument("--model", type=str, required=True, help="Name of the Model module.")
-args = parser.parse_args()
-
-
-MODEL_SFX=args.model + "_UNIQUIFIED"
-
-def bash(cmd):
-  fail = os.system(cmd)
-  if fail:
-    print(f'[*] failed to execute {cmd}')
-    sys.exit(1)
-  else:
-    print(cmd)
-
-def get_filelist(filelist):
-  fnames = []
-  with open(filelist) as f:
-    lines = f.readlines()
-    for line in lines:
-      try:
-        fname = line.split("/")[-1].strip()
-        fnames.append(fname)
-      except:
-        print(f"Something is wrong about this line '{line}'")
-  return fnames
-
-def update_filelist(cur_file, new_file):
-  bash(f"echo \"{args.gcpath}/{new_file}\" >> {os.path.join(args.gcpath, args.mod_filelist)}")
-
-def generate_copy(c, sfx):
-  (cur_name, ext) = os.path.splitext(c)
-  new_name = cur_name + "_" + sfx
-  new_file = new_name + ext
-
-  cur_file = os.path.join(args.gcpath, c)
-  new_file = os.path.join(args.gcpath, new_file)
-
-  shutil.copy(cur_file, new_file)
-  bash(f"sed -i s/\"module {cur_name}\"/\"module {new_name}\"/ {new_file}")
-  return new_file
-
-def dfs_update_modules(tree, common_fnames, visited, top_fnames):
-  # List of direct submodules to update
-  childs_to_update = list()
-  for child in tree['instances']:
-    # We don't have to change stuff that are under the dut
-    if (child['module_name'] == args.dut) or (child['module_name'] in visited):
-      continue
-    if dfs_update_modules(child, common_fnames, visited, top_fnames):
-      childs_to_update.append(child['module_name'])
-      if (child['module_name'] + ".sv") in common_fnames:
-        child['module_name'] = child['module_name'] + "_" + MODEL_SFX
-
-  cur_module = tree['module_name']
-  cur_file = cur_module + ".sv"
-  new_file = None
-
-  # cur_file is in the common list, or is a ancestor of of them, generate a new file
-  if (cur_file in common_fnames) or len(childs_to_update) > 0:
-    new_file = generate_copy(cur_file, MODEL_SFX)
-    update_filelist(cur_file, os.path.basename(new_file))
-
-  for submodule_name in childs_to_update:
-    if (submodule_name + ".sv") in common_fnames:
-      bash(f"sed -i s/\"{submodule_name}\"/\"{submodule_name}_{MODEL_SFX}\"/ {new_file}")
-
-  visited.add(cur_module)
-  return (new_file is not None)
-
-def main():
-  top_fnames = set(get_filelist(args.top_filelist))
-  mod_fnames = set(get_filelist(args.mod_filelist))
-  common_fnames = top_fnames.intersection(mod_fnames)
-
-  with open(args.model_hier_json) as imhj:
-    imhj_data = json.load(imhj)
-
-    with open(args.out_model_hier_json, "w+") as out_file:
-      visited = set()
-      dfs_update_modules(imhj_data, common_fnames, visited, top_fnames)
-      json.dump(imhj_data, out_file, indent=2)
-
-if __name__ == "__main__":
-  main()
diff --git a/scripts/uniquify-module-names.py b/scripts/uniquify-module-names.py
new file mode 100755
index 0000000000..75fc8c85db
--- /dev/null
+++ b/scripts/uniquify-module-names.py
@@ -0,0 +1,207 @@
+#!/usr/bin/env python3
+
+import json
+import argparse
+import shutil
+import os
+import sys
+
+
+parser = argparse.ArgumentParser(description="")
+parser.add_argument("--model-hier-json", type=str, required=True, help="Path to hierarchy JSON emitted by firtool. Must include DUT as a module.")
+parser.add_argument("--top-hier-json", type=str, required=True, help="Path to hierarchy JSON emitted by firtool. Must include DUT as a module.")
+parser.add_argument('--in-all-filelist', type=str, required=True, help='Path to input filelist that has all modules (relative paths).')
+parser.add_argument("--dut", type=str, required=True, help="Name of the DUT module.")
+parser.add_argument("--model", type=str, required=True, help="Name of the Model module.")
+parser.add_argument('--out-dut-filelist', type=str, required=True, help='Path to output filelist including all modules under the DUT.')
+parser.add_argument('--out-model-filelist', type=str, required=True, help='Path to output filelist including all modules under the MODEL.')
+parser.add_argument("--out-model-hier-json", type=str, required=True, help="Path to updated hierarchy JSON emitted by this script.")
+parser.add_argument('--target-dir', type=str, required=True, help='Path to where module sources are located (combined with --in-all-filelist gives the absolute path to module sources).')
+parser.add_argument("--gcpath", type=str, required=True, help="Path to gen-collateral")
+args = parser.parse_args()
+
+MODEL_SFX=args.model + "_UNIQUIFIED"
+
+
+def bash(cmd):
+  fail = os.system(cmd)
+  if fail:
+    print(f'[*] failed to execute {cmd}')
+    sys.exit(1)
+  else:
+    print(cmd)
+
+def bfs_collect_modules(tree, child_to_ignore = None):
+  q = [(tree['instance_name'], tree['module_name'], tree['instances'])]
+
+  modules = list()
+  while len(q) != 0:
+    front = q[0]
+    q.pop(0)
+
+    (inst, mod, child) = front
+    modules.append(mod)
+    for c in child:
+      if c['module_name'] != child_to_ignore:
+        q.append((c['instance_name'], c['module_name'], c['instances']))
+  return modules
+
+def get_modules_in_verilog_file(file):
+  module_names = list()
+  with open(file) as f:
+    lines = f.readlines()
+    for line in lines:
+      words = line.split()
+      if len(words) > 0 and words[0] == "module":
+        module_names.append(words[1].replace("(", "").replace(")", "").replace(";", ""))
+  return module_names
+
+def get_modules_in_filelist(verilog_module_filename, cc_filelist):
+  with open(args.in_all_filelist) as fl:
+    lines = fl.readlines()
+    for line in lines:
+      path = line.strip()
+      basepath = os.path.basename(path)
+      ext = basepath.split(".")[-1]
+
+      if (ext == "v") or (ext == "sv"):
+        modules = get_modules_in_verilog_file(os.path.join(args.gcpath, basepath))
+        for module in modules:
+          verilog_module_filename[module] = basepath
+      else:
+        cc_filelist.append(basepath)
+  return (verilog_module_filename, cc_filelist)
+
+def get_modules_under_hier(hier, child_to_ignore=None):
+  with open(hier) as hj:
+    hj_data = json.load(hj)
+    modules_under_hier = set(bfs_collect_modules(hj_data, child_to_ignore=child_to_ignore))
+  return modules_under_hier
+
+def write_verilog_filelist(modules, verilog_module_filename, out_filelist):
+  written_files = set()
+  existing_modules = verilog_module_filename.keys()
+
+  with open(out_filelist, "w") as df:
+    for module in modules:
+      if module in existing_modules:
+        verilog_filename = verilog_module_filename[module]
+        if verilog_filename not in written_files:
+          written_files.add(verilog_filename)
+          if args.target_dir in verilog_filename:
+            df.write(f"{verilog_filename}\n")
+          else:
+            df.write(f"{args.target_dir}/{verilog_filename}\n")
+  return written_files
+
+def write_cc_filelist(filelist, out_filelist):
+  with open(out_filelist, "a") as df:
+    for path in filelist:
+      file = os.path.basename(path)
+      df.write(f"{args.target_dir}/{file}\n")
+
+def generate_copy(c, sfx):
+  (cur_name, ext) = os.path.splitext(c)
+  new_name = cur_name + "_" + sfx
+  new_file = new_name + ext
+
+  cur_file = os.path.join(args.gcpath, c)
+  new_file = os.path.join(args.gcpath, new_file)
+
+  shutil.copy(cur_file, new_file)
+  bash(f"sed -i s/\"module {cur_name}\"/\"module {new_name}\"/ {new_file}")
+  return new_file
+
+def bfs_uniquify_modules(tree, common_fnames, verilog_module_filename):
+  q = [(tree['instance_name'], tree['module_name'], tree['instances'], None)]
+  updated_submodule = set()
+  existing_modules = verilog_module_filename.keys()
+
+  while len(q) != 0:
+    front = q[0]
+    q.pop(0)
+    (inst, mod, child, parent) = front
+
+    # external module
+    if mod not in existing_modules:
+      assert(len(child) == 0)
+      continue
+
+    cur_file = verilog_module_filename[mod]
+
+    # if the module is common, make a copy & update its instance in its parent
+    new_mod = mod
+    if mod in common_fnames:
+      try:
+        new_file = generate_copy(cur_file, MODEL_SFX)
+        if parent is not None and ((parent, mod) not in updated_submodule):
+          parent_file = os.path.join(args.gcpath, verilog_module_filename[parent])
+          bash(f"sed -i s/\"{mod} \"/\"{mod}_{MODEL_SFX} \"/ {parent_file}")
+          updated_submodule.add((parent, mod))
+
+        # add the uniquified module to the verilog_modul_filename dict
+        new_mod = mod + "_" + MODEL_SFX
+        verilog_module_filename[new_mod] = new_file
+      except:
+        print(f"No corresponding file for {cur_file}")
+
+    # traverse its children
+    for c in child:
+      if c['module_name'] != args.dut:
+        q.append((c['instance_name'], c['module_name'], c['instances'], new_mod))
+
+def dfs_update_modules(tree, common_fnames, visited):
+  # List of direct submodules to update
+  childs_to_update = list()
+  for child in tree['instances']:
+    # We don't have to change stuff that are under the dut
+    if (child['module_name'] == args.dut):
+      continue
+    if dfs_update_modules(child, common_fnames, visited):
+      childs_to_update.append(child['module_name'])
+      if (child['module_name']) in common_fnames:
+        child['module_name'] = child['module_name'] + "_" + MODEL_SFX
+
+  cur_module = tree['module_name']
+  new_file = None
+
+  # cur_file is in the common list, or is a ancestor of of them, generate a new file
+  if (cur_module in common_fnames) or len(childs_to_update) > 0:
+    new_file = 1
+
+  visited.add(cur_module)
+  return (new_file is not None)
+
+def uniquify_modules_under_model(modules_under_model, common_modules, verilog_module_filename):
+  with open(args.model_hier_json) as imhj:
+    imhj_data = json.load(imhj)
+    visited = set()
+    bfs_uniquify_modules(imhj_data, common_modules, verilog_module_filename)
+    dfs_update_modules  (imhj_data, common_modules, visited)
+
+    with open(args.out_model_hier_json, "w+") as out_file:
+      json.dump(imhj_data, out_file, indent=2)
+
+def main():
+  verilog_module_filename = dict()
+  cc_filelist = list()
+  get_modules_in_filelist(verilog_module_filename, cc_filelist)
+
+  modules_under_model = get_modules_under_hier(args.model_hier_json, args.dut)
+  modules_under_top   = get_modules_under_hier(args.top_hier_json)
+  common_modules      = modules_under_top.intersection(modules_under_model)
+
+  # write top filelist
+  write_verilog_filelist(modules_under_top, verilog_module_filename, args.out_dut_filelist)
+
+  # rename modules that are common
+  uniquify_modules_under_model(modules_under_model, common_modules, verilog_module_filename)
+  uniquified_modules_under_model = get_modules_under_hier(args.out_model_hier_json, args.dut)
+
+  # write model filelist
+  write_verilog_filelist(uniquified_modules_under_model, verilog_module_filename, args.out_model_filelist)
+  write_cc_filelist     (cc_filelist, args.out_model_filelist)
+  
+
+if __name__=="__main__":
+  main()
diff --git a/variables.mk b/variables.mk
index 1f659ac7ca..443caa94a9 100644
--- a/variables.mk
+++ b/variables.mk
@@ -186,10 +186,6 @@ MODEL_MODS_FILELIST ?= $(build_dir)/$(long_name).model.f
 # list of all blackbox files (may be included in the top/model.f files)
 # this has the build_dir appended
 BB_MODS_FILELIST ?= $(build_dir)/$(long_name).bb.f
-# top blackbox module files to include
-TOP_BB_MODS_FILELIST ?= $(build_dir)/$(long_name).top.bb.f
-# model blackbox module files to include (not including top blackbox modules)
-MODEL_BB_MODS_FILELIST ?= $(build_dir)/$(long_name).model.bb.f
 # all module files to include (top, model, bb included)
 ALL_MODS_FILELIST ?= $(build_dir)/$(long_name).all.f
 
diff --git a/vlsi/Makefile b/vlsi/Makefile
index 8259e7a6ec..ad51c75443 100644
--- a/vlsi/Makefile
+++ b/vlsi/Makefile
@@ -72,7 +72,7 @@ VLSI_RTL = $(build_dir)/syn.f
 ifneq ($(CUSTOM_VLOG), )
 	RTL_DEPS = $(CUSTOM_VLOG)
 else
-	RTL_DEPS = $(TOP_MODS_FILELIST) $(TOP_BB_MODS_FILELIST) $(TOP_SMEMS_FILE)
+	RTL_DEPS = $(TOP_MODS_FILELIST) $(TOP_SMEMS_FILE)
 endif
 
 $(VLSI_RTL): $(RTL_DEPS)
@@ -80,7 +80,7 @@ ifneq ($(CUSTOM_VLOG), )
 	> $(VLSI_RTL)
 	$(foreach file,$^,echo $(file) >> $(VLSI_RTL))
 else
-	cat $(TOP_MODS_FILELIST) $(TOP_BB_MODS_FILELIST) | sort -u > $(VLSI_RTL)
+	cat $(TOP_MODS_FILELIST) | sort -u > $(VLSI_RTL)
 	echo $(TOP_SMEMS_FILE) >> $(VLSI_RTL)
 endif
 
diff --git a/vlsi/sim.mk b/vlsi/sim.mk
index 13a7fcc3e0..291c93adf6 100644
--- a/vlsi/sim.mk
+++ b/vlsi/sim.mk
@@ -10,7 +10,7 @@ $(SIM_CONF): $(sim_common_files)
 	echo "  top_module: $(VLSI_TOP)" >> $@
 	echo "  tb_name: ''" >> $@  # don't specify -top
 	echo "  input_files:" >> $@
-	for x in $$(cat $(MODEL_MODS_FILELIST) $(MODEL_BB_MODS_FILELIST) | sort -u) $(MODEL_SMEMS_FILE) $(SIM_FILE_REQS); do \
+	for x in $$(cat $(MODEL_MODS_FILELIST) | sort -u) $(MODEL_SMEMS_FILE) $(SIM_FILE_REQS); do \
 		echo '    - "'$$x'"' >> $@; \
 	done
 	echo "  input_files_meta: 'append'" >> $@