You can't exclude folders from scanning which means that any sub-folders of a selected folder will be scanned (hidden content is skipped though). Also deselecting folders from scanning doesn't remove files from those folders from the Library. So you may have inadvertently scanned those folders at some point.

Make sure that they're not selected for scanning nor Folder Monitoring under File > Add/Rescan Files dialog. Then just remove the offending folders from the Music > Location node in the Media Tree (select only from Library if prompted).

I run MM4 on a win10 machine. My Music Library is on my Synology NAS. I access it as a mapped drive M:\. Under M:\ there are several directories, Including
M:\#recycle
M:\#snapshot
M:\Automatically add to iTunes
M:\iTunes
M:\iTunes\iTunes Media
M:\iTunes\iTunes Media\Music\
etc....

During setup of Media Monkey, when specifying the folders I want to scan for media files, I select ONLY:

M:\iTunes\iTunes Media\Music


I didn't specify any other folders. However, Media Monkey is now picking up all the files in the M:\itunes\itunes Media\Music, as well as in the M:\#snapshot folder, and listing them in My Music, since the #snapshot folder is a backup directory, I now have boatloads of duplicate entries. It's making my music library completely unmanageable. I can't seem to find any place to specify for Media Monkey to exclude #snapshot folder.

I can't seem to find any reference to excluding folders from search in the help.

Any suggestions before I go crazy?

Dan