Depending on the sophistication of the malware in question, there is no certainty your 'corrupted' files can be cured/cleaned, but, after clearing your temp files, perhaps you can restore the files from an earlier version?
Try in order:
TFC (TempFileCleaner from bleepingcomputer)
RogueKiller (bleepingcomputer)
MalwareBytes AntiRootkit
MalwareBytes AM
AdwCleaner (Bleepingcomputer)
Then left click on a file you'd like to recover, select properties, see if any previous versions exist from restore points....
Sometimes files can be encrypted /destroyed thoroughly, other times they are simply hidden, and can be recovered; however, sometimes, there might be no escaping a loss of data, deleting partitions, and reformatting/reinstalling OS...