Renaming files is an issue for me. I will do as @mudgel suggested.
 
What I do from the Sonar Browser is; Open the Project Audio Folder and right click on a wav, and select the option to delete. Files being used in the currently open project errors back with a message that says it cannot be deleted.
This got to me because each time a synth is frozen/unfrozen-then frozen again a new wav is created.

The Save As technique is impractical if you haven't been doing it all along. I have close to 100 projects on my audio drive and never thought to do that as I went along.  I really wish the Clean Audio worked but it's way to risky. This was brought up a few months ago in a thread.
http://forum.cakewalk.com/Platinum-Clean-Audio-Folder-problem-or-not-m3163441.aspx#3163593.  Keith Albright said they would look into it. I very much hope they do as I would love a SAFE way to clean all the bits of audio junk.

Well it's good news to hear that they are going to look at it.
The CWAF tools is ok, but at very least it would be easier if I could just select the folder/folders I wanted to scan instead of selecting a drive and then excluding all the folders I don't want to scan.

I'll agree that a better system of managing files would be a popular feature addition. 
Because new hard drives are so large it's not an issue for me. I stopped worrying about my computers storage when 500 Gig drives came out.  This might be more of an issue for folks who are always starting new projects and not finishing old ones.  
I work album to album and those albums sometimes take a year, but they do get finished and then archived to Data drives. I use the "save as" for the final archive version and they take up very little room after that. I would use this new improved clean up feature if it existed and then just drag and drop the folder, would be faster. 
 
A little tip to help keep unwanted junk out of the audio folder. I find that if you don't delete a bad take, that Sonar stores it forever. It becomes a hidden layer I guess just in case you want to go back. I never do. I want it gone... I think this is another bad habit people get into.. take hoarding.  
 
So when I'm recording my self or a band and make false starts or finish a take and don't like that one I actually delete the track(s). If you  use record "overwrite" the original is still going to be in the audio folder. So deleting bad takes will keep only the good ones in the audio folder. 
I know it takes a few seconds to delete a track but possibly this is the ultimate solution to messy audio folders. 
 

Cactus Music
I find that if you don't delete a bad take, that Sonar stores it forever.

That should only happen if you save the project with the takes still referenced at some point. If you delete takes before saving, SONAR will delete all the unreferenced files when you close the project. But if you're in that habit of saving regularly while working or have Autosave enabled, that may never be the case.

Looks like someone in another thread dropped their subscription because, at least in part, of this:
 
"The whole experience of Platinum installing numerous 32 Bit Plugins on my 64 Bit PC plus piles of unwanted DXi's did not float my boat. Added to the complete inability to clean projects of unwanted audio files without a search of entire system just added to the pain."
 
They really should bring it up to date. It doesn't seem like it would be a very big deal to redo it.
 
It would work for me if the CWAF tool allowed me to choose the directory I wanted to scan, or the browser flagged the files that were in use in the project, and allowed me to simply delete the ones that weren't.

brundlefly

Cactus Music
I find that if you don't delete a bad take, that Sonar stores it forever.

That should only happen if you save the project with the takes still referenced at some point. If you delete takes before saving, SONAR will delete all the unreferenced files when you close the project. But if you're in that habit of saving regularly while working or have Autosave enabled, that may never be the case.

Yes Dave this must be it as I often do hit save and then decide to delete. Never thought of that so thanks for the clarification. 
And I also think it makes a difference now if you use Comping mode. I think that keeps everything. The old Sonar defaulted to Sound on Sound. now it defaults to Comping which is better, but I prefer Overwrite being old school stubborn with unreasonable habits. 

I'd have to double-check, but I don't think Comp recording is any different. Possibly the difference you're seeing is more about Loop recording. When you loop record, only a single file is created with the "takes" referencing different sections of the file. So if you save the project with even one of the takes from that recording pass still present, the file is still referenced. And/or maybe it happens because you miss one of the "leftovers" created by the auto-split that happens with the last partial take when you're deleting.