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I have scheduled Microsoft Security Essentials (on Windows 7) to scan my whole hard drive every night at 2 a.m. When I start using my computer in the morning, the scan is complete, but the whole system is slow for the first few minutes of use. I presume that this is because reading every file on disk causes Windows to remove many things that would otherwise be in the system file cache, or page memory that would otherwise be resident out to disk.

Is there a way to counteract this? I would love it if, after the scan were over, my computer would start returning desktop application pages back into physical memory and caching frequently used files.

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You could substitute your own scheduled task for the MSE one, executing a batch file commanding MSE to run its scan, and then a restart command. This should bring back the Windows Prefetch items into memory, ready for you to use in the morning.

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That's a good idea, although I would love to be able to do this without restarting and potentially losing any unsaved data that's in a running application. – Michael Hoffman Feb 7 '12 at 19:50

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