Telling the Clean Audio Folder tool to find unused audio tracks in your project causes it to scan the EVERY HARD DRIVE ON YOUR SYSTEM. This takes ages. There is no way of stopping it.
 
And it does this despite having set the the project directory, despite having told it to recurse below this directory only, and despite having set the Use Per-Project Audio Folders preference.
 
Yes, I know what it is doing and why (but it is not made clear on the dialog, nor in the help). This made sense back when hard drives were small and multiply-used audio files were one way to save space. But not now, with terrabyte drives and per-project audio folders being the norm. By all means, warn the user of possible multiple use. Add the full scan as an option. But please, don't make it the standard behavior. 
 
Either bring it into the 21st century or just remove it from the menu. 
 
It even scans the Recycling bin, for goodness sake! Who's gonna put projects in there?!?

+1 I agree with you totally. I don't have enough courage to ignite Clean Audio Folder tool in my 8 TB system.

Yes Cake. Please give us the option to specify which drive\folder to scan!

The CWAF tool is more effective, though that too could do with an update.

+1 CWAF as you can specify excluded directories, though it would be nicer to specify included directories. 

+ 1... It's a shame how amateur it is... Plus the naming scheme, wich is ridiculous... In Cubase, if you record something to a track named "kick", the result will be a file called kick.wav... And if u run the clean audio in Cubase it is really fast and reliable, no mather how many "kicks.wav" you have and your computer... If the one you recorded in that specific projet was deleted from it, when you choose to clean, Cubase will erase it either from the project or from the hard disk... I never had a single problem with this operation in Cubase.

Peace out my friends!

Yes Cake. Please give us the option to specify which drive\folder to scan!

I asked for this as far back as 1999, default to the current project's folder; optionally examine the rest of the computer.  I used to do the per-project folders thing (by hand) before there was a SONAR. It would drive me nuts that it would insist on searching everything. Let's keep our fingers crossed. 

Is this a joke? LOL - I was just about to search for this functionality. I simple can't believe it's so catastrophically useless? How does something like this get past quality control? 

I've never used it.

The best way (and also the most time consuming) is to do a "save as" of ALL your projects to a completely different folder, making sure that "copy audio with project" is selected with every save.

Once this is done you can go back and delete all the original project folders.

You will of course do a full backup of your old projects before deleting

My day job is Avionics Software Engineer, however I have done some Windows SW development over the years.  IMO, this would be (pun intended) a "Cakewalk" of a fix; the addition of a search scope selection feature. 

It could just put up a tree view of the PC with check boxes pre-checked as defaults for the current open project's folders and the shared audio folder. Then the user could chose to expand the scope by "checking" folders or the entire PC if they wanted - like the interface you see on most backup programs.