Once the concept of metadata has been embraced, users invariably want to fix the subfolder hell they inherited / created. Sometimes it’s easier to just create the library again and start over, but that’s not always possible and sometimes you need to fix the library where it is.
Extracting the metadata from the subfolders currently on the site is easy though, simply export the library to Excel.
Click in the subfolders one at a time, go to Quick Edit / Datasheet View, and bulk tag them.
Once all the documents have been reclassified using metadata, you need to move the documents out of the subfolders to library level. Go to Content and Structure, select the subfolder in the library so the documents display on the right. Select all the documents then Actions and Move, and move them one level up.
It’s quite the mission, so use metadata instead from the beginning and just avoid all this. 😉