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I would like to prevent them from even coming up if possible. I don't know why Windows doesn't use the %system root%\temp folder for these. :(

Looks like there have been a couple others asking about the same issue but the answer is just take ownership and delete, which would be fine if it were just 1 or 2 stations but I'm looking at possibly hundreds of them. Would there be a way to script a removal of these and force Windows into using the Temp folder?

Similar issue, How do I delete left-over Windows Update folders?

Thanks, Joel

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keep in mind, these files are often there to provide uninstallation, –  Frank Thomas Sep 9 '13 at 19:48
    
These are not the un-installation ones. These are in the root of C:\ and are supposed to be automatically removed after the patch or update is finished installing. Check out the known issues on this .net patch for what I'm referring to, support.microsoft.com/kb/951847/en-us –  Joel Sep 10 '13 at 0:06

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