I haven't seen any DRM protected MP3 files.

As for DRM protected Windows Media .WMA audio files and .WMV video files you may remove DRM protection using lossless DRM removal software like FairUse4WM or lossy DRM removal software like Tunebite.

As for lossless DRM removal software, I don't see any problem using it for a folder with DRM protected and DRM-free files. As for lossy DRM removal software, say, Tunebite can automatically find DRM protected media files in the selected folders.

p.s. Please note that DRM removal software needs valid licenses that allows you to play audio and video files. Please use it for personal backups only.