What CCleaner does
CCleaner deletes any Prefetch file older then two weeks based on the .pf file's last access date. This is completely idiotic for a number of reasons. First you should never delete a .pf for any installed application. With the .pf file missing, that application will take up to 100% more time to load when you decide to launch it. CCleaner does this to any application you have installed on your computer but have not used in over two weeks. It makes absolutely no sense to delete these files. Why would you deliberately want to slow down any installed application's load time? It will also do this if you have not used you computer for two weeks. Second, it is quite common to disable the NTFS Last Access Time Stamp for performance reasons. I actually recommend doing this since it speeds up the file system. In this case CCleaner will delete any .pf file that was created over two weeks ago. You can clearly see how running CCleaner in this case would wind up deleting ALL your Prefetch files every two weeks. Now you are crippling every application's load time on your system instead of just the ones you have not used in two weeks. Ridiculous!

Testing
Make sure the Task Scheduler service is set to automatic. Launch an application like Firefox three times. Reboot and make sure there is a FIREFOX.EXE-XXXXXXXX.pf file in the C:\WINDOWS\Prefetch folder. If there is, launch Firefox and time it. Then delete the .pf file, reboot, relaunch Firefox and time it again. You will now see Firefox take a significantly longer time to load. Now imagine this on any other application, then imagine doing this deliberately every two weeks? Why? To save a tiny bit of HD space? It makes no sense. 128 .pf files take up maybe 5 MB of disk space.

Conclusion
Do not clean the prefetch folder! If you use CCleaner uncheck the "Old Prefetch Data" option. Finally let the makers of CCleaner know they need to remove this option from CCleaner. For more information read: