I've done something similar a while back. It's not exactly elegant, but it gets the job done. Here's an outline of the procedure:
1. In MC highlight all files that are in that folder. Presumably this includes all subfolders as well. The FILES view is probably the best one to use for this.
2. Open Rename Move and Copy Files tool. Set RM&C to MOVE all selected files to a new folder that is outside of the original. I.E. if your folder is D:\Music , move it to something like D:\TEMPMUSIC . Details of how to do this are left to the reader.
3. After pressing "OK", MC should move all the files, relatively instantly. Now your original folder should be empty. If it is not empty, the files left over were not part of MC's Library. Now you have them isolated by themselves.
4. Do something with these "extra" files. Delete them, move them to a different folder, rename the existing folder, etc.
5. Your existing files, that are in your temporary folder, should still be highlighted. If not, highlight them again. Open RM&C. Now move them back to the original location, which should be EMPTY to start.
When you finish, the folder should only contain files that MC knows about.
There are many caveats here. You should probably try this with a single Album as a test. One of the biggest caveats is the "move all files in folder" check box. Brief documentation is here:
https://wiki.jriver.com/index.php/Rename,_Move,_and_Copy_Files#Files_That_Will_Be_ProcessedIn short, you want this ON if you have images, rip logs, or any other extra files in your album directories that MC has not strictly imported. In my case this makes sure that my album art work (which is in the same folder as each album) and my disk rip logs get moved.
Experiment a bit first. Go slow. Start with one file. Then one album. Only do more when you are confident with your results. This procedure has worked for me, but only you can determine if it will work correctly for your collection and your file layout.
Best of luck,
Brian.