Well as descussed above, leave out the system folders and maybe keep it simple...ie start menu folders. Also as this is only doing the start menu (if its not expanded to do the whole computer), then it wont have to search GB/TBs of data.
I know for a fact that my start menu is filled with empty folders as lots of installers tend to just not delete the folders they have made. If applications need a folder for writing, they generally just make another folder and get on with it.
Heres your chance to try and get this idea that you previously wanted taken action..shows at least two people wanted it.