Use Tools > Cakewalk Audio Finder instead. CWAF searches only the drive you select and allows excluding folders on that drive. Plus it will clean every per-project folder on one go. Not perfect, but far more flexible and informative than Clean Audio Folder.

Used it a couple of times early on in X1, then I remember trying it again in X3. I haven't had a go with Platinum, I just want it to clean up one 500MB project folder after a long mix session with a particular song, not search my entire 3TB of storage space just to get rid of a couple of .wav files.
I'm with sharke on this one, 'save as' to a new project, then delete the old one manually. Not ideal but much quicker.

gswitz
What sharke said.

 
What Geoff said about Sharke.

jb101

gswitz
What sharke said.

 
What Geoff said about Sharke.

What jb101 said about what Geoff said about Sharke.

http://forum.cakewalk.com/Its-time-for-Clean-Audio-Folder-and-CWAF-to-mature-please-m3170417.aspx