There has been much written about clearing PreFetch Folder.
I hold the opinion that it is not a good idea and no useful purpose is served.
Have a quick read here, to see generally where I'm coming from with my disagreement:
http://www.edbott.com/weblog/archives/000743.html
and for a more detailed (and better, IMO) description read the section by Mark Russinovich (SysInternals) related to PreFetch and how it functions as a list of lists and a directory for defragging ( without loading a single "file" into Memory before an application is called).
http://msdn.microsoft.com/en-us/magazine/cc302206.aspx
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On the other hand, a user will not "harm" anything by clearing Prefetch, simply because Windows will resume building the very same selection of lists back into Prefetch over time and usage of your various preferred applications. The only thing even close to "harm" is that it will take longer for applications to load because they won't benefit from the ready-made .pf list of what should be called for and where to find the called files.
Initial Loading of applications will most likely be "slower" after clearing PreFetch, but only the first time after clearing Prefetch, However, loading time will improve even more by leaving the items in PreFetch because Defrag utilities will reference to the PreFetch folder when doing their work of laying out continuous sections for commonly used applications and making them more readily available earlier on the hard disk.
Prefetch is by default "self cleaning" in that Windows only allows 128 items into the Folder and when a new application needs to be listed, it will push out the oldest/least used item.
I presently have 59 items in my C:\Windows\Prefetch and none of them are older than 12/27/08.
I'd say that is pretty "up to date" with nothing hanging around as old clutter.
And I have never cleared the Prefetch Folder on this machine.
I have cleared the Prefetch Folder on other test machines, and have noticed the increased lag in loading applications.
Your mileage may vary.
And I'm certainly open to learning from others if there is something I'm overlooking here.
Best Regards,
Doug