diff --git a/common.mk b/common.mk
index a4668075..ed02a10e 100644
--- a/common.mk
+++ b/common.mk
@@ -243,6 +243,12 @@ $(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(ALL_MODS_FILELIST) $(BB_MODS_FILEL
 	$(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) \
+		--dut $(TOP)
 	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)
diff --git a/scripts/uniqify-module-names.py b/scripts/uniqify-module-names.py
index 7269c63f..a88d4147 100755
--- a/scripts/uniqify-module-names.py
+++ b/scripts/uniqify-module-names.py
@@ -14,7 +14,6 @@ parser.add_argument("--mod-filelist", type=str, required=True, help="Abs path to
 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('--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()
 
 
@@ -33,6 +32,9 @@ def get_filelist(filelist):
 
   return fnames
 
+def update_filelist(cur_file, new_file):
+  sh.sed("-i", f"s/\b{cur_file}\b/{new_file}/", os.path.join(args.gcpath, args.mod_filelist))
+
 
 def generate_copy(c, sfx):
   (cur_name, ext) = os.path.splitext(c)
@@ -43,43 +45,45 @@ def generate_copy(c, sfx):
   new_file = os.path.join(args.gcpath, new_file)
 
   shutil.copy(cur_file, new_file)
-  sh.sed("-i", f"s/{cur_name}/{new_name}/", new_file)
-
+  sh.sed("-i", f"s/\b{cur_name}\b/{new_name}/", new_file)
   return new_file
 
 
 
-def dfs_update_modules(tree, common_fnames, visited):
+def dfs_update_modules(tree, common_fnames, visited, top_fnames, updated_modules):
   # 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):
+    if dfs_update_modules(child, common_fnames, visited, top_fnames, updated_modules):
       childs_to_update.append(child['module_name'])
+      if (child['module_name'] + ".sv") in common_fnames:
+        child['module_name'] = child['module_name'] + "_Model"
+        updated_modules.append(child['module_name'])
 
   cur_module = tree['module_name']
   cur_file = cur_module + ".sv"
   new_file = None
 
   # cur_file is in the common list, generate a new file
-  for c in common_fnames:
-    if cur_file == c:
-      new_file = generate_copy(c, "Model")
+  if cur_file in common_fnames:
+    new_file = generate_copy(cur_file, "Model")
+    update_filelist(cur_file, os.path.basename(new_file))
 
   # has some child to update, but new_file wasn't generated
   if (new_file is None) and len(childs_to_update) > 0:
-    if cur_module == args.model:
-      new_file = os.path.join(args.gcpath, cur_file)
-    else:
-      new_file = generate_copy(cur_file, "Model")
+    new_file = os.path.join(args.gcpath, cur_file)
+    assert(cur_file not in top_fnames)
 
   if new_file is not None:
     print(f"-- {cur_module}")
 
   for submodule_name in childs_to_update:
     print(f"|- {submodule_name}")
-    sh.sed("-i", f"s/{submodule_name}/{submodule_name}_Model/", new_file)
+    if (submodule_name + ".sv") in common_fnames:
+      sh.sed("-i", f"s/\b{submodule_name}\b/{submodule_name}_Model/", new_file)
 
   visited.add(cur_module)
   return (new_file is not None)
@@ -88,16 +92,18 @@ def dfs_update_modules(tree, common_fnames, visited):
 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)
-  for c in common_fnames:
-    print(c)
 
   imhj = open(args.model_hier_json, "r")
   imhj_data = json.load(imhj)
 
   visited = set()
-  dfs_update_modules(imhj_data, common_fnames, visited)
+  updated_modules = list()
+  dfs_update_modules(imhj_data, common_fnames, visited, top_fnames, updated_modules)
+
+  out_file = open(args.model_hier_json, "w")
+  json.dump(imhj_data, out_file, indent=2)
+  out_file.close()