Use the Windows CHKDSK utility to do a thorough scan of the volume(s). Then use the Windows defrag utility to de-fragment the volumes. If the drives are severely fragmented, run the defrag several times. If Windows cannot de-fragment the volume(s) effectively because of a fragmented MFT, a drive that is reaching capacity, etc., use a third-party de-fragmentation utility to run a boot-time defrag.