diff --git a/scripts/Tools/case.build b/scripts/Tools/case.build
index 394e8d3c656..3e94c4db0e6 100755
--- a/scripts/Tools/case.build
+++ b/scripts/Tools/case.build
@@ -60,7 +60,9 @@ OR
 
     CIME.utils.handle_standard_logging_options(args)
 
-    return args.caseroot, args.sharedlib_only, args.model_only, args.clean, args.clean_all
+    cleanlist = args.clean if args.clean is None or len(args.clean) else comps
+
+    return args.caseroot, args.sharedlib_only, args.model_only, cleanlist, args.clean_all
 
 ###############################################################################
 def _main_func(description):
diff --git a/utils/python/CIME/SystemTests/system_tests_common.py b/utils/python/CIME/SystemTests/system_tests_common.py
index bdcec2261c9..c8a09c1c683 100644
--- a/utils/python/CIME/SystemTests/system_tests_common.py
+++ b/utils/python/CIME/SystemTests/system_tests_common.py
@@ -118,7 +118,7 @@ def build_indv(self, sharedlib_only=False, model_only=False):
                          sharedlib_only=sharedlib_only, model_only=model_only)
 
     def clean_build(self, comps=None):
-        build.clean(self._case, cleanlist=comps)
+        build.clean(self._case, cleanlist=comps if comps is not None else [])
 
     def run(self):
         """
diff --git a/utils/python/CIME/build.py b/utils/python/CIME/build.py
index e58e0e7bf43..6e5c9d0463a 100644
--- a/utils/python/CIME/build.py
+++ b/utils/python/CIME/build.py
@@ -508,21 +508,32 @@ def _build_model_thread(config_dir, compclass, caseroot, libroot, bldroot, incro
     for mod_file in glob.glob(os.path.join(bldroot, "*_[Cc][Oo][Mm][Pp]_*.mod")):
         shutil.copy(mod_file, incroot)
 
+def cleantree(base, ignoredirs=None):
+    """
+    clean all files below base level, leave directories and top level files
+    """
+    ignoredirs.append(base)
+    for root, _, files in os.walk(base, topdown=False):
+        if root not in ignoredirs:
+            for name in files:
+                os.remove(os.path.join(root, name))
+
+
 ###############################################################################
 def clean(case, cleanlist=None, clean_all=False):
 ###############################################################################
     caseroot = case.get_value("CASEROOT")
-    if clean_all or cleanlist is not None and len(cleanlist) == 0:
+    if clean_all:
         # If cleanlist is empty just remove the bld directory
         exeroot = case.get_value("EXEROOT")
         if os.path.isdir(exeroot):
-            logging.info("removing directory %s" %exeroot)
-            shutil.rmtree(case.get_value("EXEROOT"))
+            logging.info("cleaning directory %s" %exeroot)
+            cleantree(exeroot, ignoredirs=[os.path.join(exeroot,"lib")])
         # if clean_all is True also remove the sharedlibpath
         sharedlibroot = case.get_value("SHAREDLIBROOT")
-        if clean_all and os.path.isdir(sharedlibroot):
-            logging.info("removing directory %s" %sharedlibroot)
-            shutil.rmtree(sharedlibroot)
+        if sharedlibroot != exeroot and os.path.isdir(sharedlibroot):
+            logging.warn("cleaning directory %s" %sharedlibroot)
+            cleantree(sharedlibroot)
     else:
         debug           = case.get_value("DEBUG")
         use_esmf_lib    = case.get_value("USE_ESMF_LIB")