diff --git a/mkconcore.py b/mkconcore.py
index f2fb6f7..5b0286a 100644
--- a/mkconcore.py
+++ b/mkconcore.py
@@ -789,8 +789,9 @@ def cleanup_script_files():
         containername,sourcecode = nodes_dict[node].split(':')
         if len(sourcecode)!=0 and sourcecode.find(".")!=-1: #3/28/21
             dockername,langext = sourcecode.rsplit(".", 1)
-            fbuild.write("mkdir docker-"+dockername+"\n")
-            fbuild.write("cd docker-"+dockername+"\n")
+            dockerbuilddir = "docker-"+dockername.replace("/", "__").replace("\\", "__")
+            fbuild.write("mkdir "+dockerbuilddir+"\n")
+            fbuild.write("cd "+dockerbuilddir+"\n")
             fbuild.write("cp ../src/Dockerfile."+dockername+" Dockerfile\n")
             #copy sourcefiles from ./src into corresponding directories
             fbuild.write("cp ../src/"+sourcecode+" .\n")
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 4723002..33316a7 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -153,6 +153,36 @@ def test_run_command_subdir_source(self):
             self.assertEqual(result.exit_code, 0)
             self.assertTrue(Path('out/src/subdir/script.py').exists())
 
+    def test_run_command_docker_subdir_source_build_paths(self):
+        with self.runner.isolated_filesystem(temp_dir=self.temp_dir):
+            result = self.runner.invoke(cli, ['init', 'test-project'])
+            self.assertEqual(result.exit_code, 0)
+
+            subdir = Path('test-project/src/subdir')
+            subdir.mkdir(parents=True, exist_ok=True)
+            shutil.move('test-project/src/script.py', subdir / 'script.py')
+
+            workflow_path = Path('test-project/workflow.graphml')
+            content = workflow_path.read_text()
+            content = content.replace('N1:script.py', 'N1:subdir/script.py')
+            workflow_path.write_text(content)
+
+            result = self.runner.invoke(cli, [
+                'run',
+                'test-project/workflow.graphml',
+                '--source', 'test-project/src',
+                '--output', 'out',
+                '--type', 'docker'
+            ])
+            self.assertEqual(result.exit_code, 0)
+
+            build_script = Path('out/build').read_text()
+            self.assertIn('mkdir docker-subdir__script', build_script)
+            self.assertIn('cp ../src/Dockerfile.subdir/script Dockerfile', build_script)
+            self.assertIn('cp ../src/subdir/script.py .', build_script)
+            self.assertIn('cp ../src/subdir/script.iport concore.iport', build_script)
+            self.assertIn('cd ..', build_script)
+
     def test_run_command_shared_source_specialization_merges_edge_params(self):
         with self.runner.isolated_filesystem(temp_dir=self.temp_dir):
             Path('src').mkdir()