diff --git a/tools/make-module.py b/tools/make-module.py
index 9c662ffb32..38cdf06859 100755
--- a/tools/make-module.py
+++ b/tools/make-module.py
@@ -17,9 +17,13 @@ def fix_string(input, modname):
         .replace("SCRATCH", modname.upper())
 
 
-def copy_dir(source, dest, modname):
+def copy_dir(source, dest, modname, top=True):
     for x in os.listdir(source):
-        if x == ".svn" or x == 'CMakeLists.txt':
+        if x == ".svn" or x == 'ModuleBuild.cmake':
+            continue
+        # We only want the top-level cmake file (for out of tree modules);
+        # the rest are auto-generated
+        if x == "CMakeLists.txt" and not top:
             continue
         if x.endswith(".pyc"):
             continue
@@ -29,14 +33,15 @@ def copy_dir(source, dest, modname):
         if os.path.isdir(xspath):
             xdpath = os.path.join(dest, x)
             os.mkdir(xdpath)
-            copy_dir(xspath, xdpath, modname)
+            copy_dir(xspath, xdpath, modname, top=False)
         else:
             xdpath = os.path.join(dest, fix_string(x, modname))
             with open(xspath, 'r') as fh:
                 input = fh.read()
             if xspath.endswith(".cpp") or xspath.endswith(".h") \
                     or xspath.endswith(".i-in") or xspath.endswith(".py") \
-                    or xspath.endswith(".md"):
+                    or xspath.endswith(".md") \
+                    or xspath.endswith("CMakeLists.txt"):
                 output = fix_string(input, modname)
             else:
                 output = input