Follow these steps to delete files from local machine.
1. Close Workbench ES2 (if already opened)
2. Goto C:\Users\<YOUR_USER_NAME>\Workbench ES2\<APP_SERVER_NAME>\<APPLCIATION_NAME>\<VERSION>
3. Delete the files which you no more required.
4.Open Workbench ES2 and click refresh on seletec application.
You will get rid of the "Cannot delete" problem.
Nith