Restoring impartial Windows 7 registry & OS files [closed]

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http://askubuntu.com – I use Linux personally but do repair work on windows os, mostly virus removal and repair. We keep coming up with the same issue. We believe it's the result of partially damaged or corrupted registry files or OS files. While we are able to disable and remove any virus/male-ware/spy-ware/ect, many basic OS/registry processes seem to be problematic. We have used every tool and DOS command we are aware of, but none of them seem to resolve the issue. The most common issues are hidden program files. While we can find the file path, the folders are all empty. Despite the use of unhide and registry (HowTos)