Update: This feature has been added into the upcoming Mezzmo v5.0. Simply add an _ignore.mezzmo file into a folder and Mezzmo will not include the folder, it's files and sub-folders into your Mezzmo library.

To create an _ignore.mezzmo file, use Windows Explorer to right-click in the folder and click New -> Text Document and then rename the newly created file as _ignore.mezzmo.