Common reasons why some files do not get removed on uninstall The components to which these files belong are marked as permanent. Check the attribute column of the components table . Components to which these files belong do not have a component GUIDs. Components without GUID are not managed by Windows Installer. If the keypath of the component has a shared DLL refcount, then the component will not be uninstalled. If the component is installed in the system folder and at the time of uninstallation there is an external shared DLL refcount for any one file in the component, then the component will not be uninstalled. You can use the wise interal remove file table to remove such files / folders or use WiseScript / VB Script to remove them.