Go to your login screen, and from the drop down list select add application.
From the popup window select the application you want to delete and select the delete option.
1) Check if the FDM database schema was cleared, if not you might need to drop all the tables of the schema. These tables will be recreated when you create a new FDM app.
2) Delete the FDM file share
3) Delete the FDM application from Shared Services (Application Library->FDM-> ... your FDM app name)