You have a few options as I see it. You can drag and drop the folders from explorer to MC, and then choose to import the files.
You can select the whole disk for import (auto or manual), and exclude the few directories you don't want.
Or you can do it one folder at a time.
I'll have to say that you have a pretty strange setup if you have thousands of folders, not nested or anything. Perhaps it's about time you consider moving the folders under a few media subtype specific directories? I can not see a single reason why someone would have thousands of directories one the root on one or several disks for instance. Remember that importing one directory always includes the directories underneath the selected directory as well.