Remove Builds, Enterprise Extensions, and Source Control folders from Project Areas

I would like to know is there any way to remove Builds, Enterprise Extensions, and Source Control folders from project areas in CLM? I want to remove the folders before a new project area is created so they will not show up in the project area at all. I tried to remove them from the from the process template so they are not automatically created when I create the new project areas, but that was unsuccessful. If there is anyway these folders can be removed I would appreciate the help.