Project folders are not deleted unless they were placed in any of windows temporary locations.
Also depends on what options you had set in CCLEANER.
Without knowing that it is too much guesswork at this end.
Always better to leave at the default unless you know what you are doing.
Normally it uses "Normal file deletion" which means that there is a good chance of recovering the folders.
If it was set for secure then you would need a third party piece of software to dig out any files and that is not a job for the faint of heart.
Really you haven't given much to go on other than saying it was CCLEANER.
I use it on a daily basis in development work to give me a clean start and drop all my cache etc. and have never lost files.
One of the easier pieces of software to bring back files is "RECUVA" but even with that you need to be tech savvy.
Whenever I tell anyone to use CC I always say leave at the default settings.
Are you 100% certain it was CC that did it ?
EDIT
ADDITIONAL INFO