How to apply rules only to subfolders

I thought it wouldn't be appropriate to post under the sticky located here: viewtopic.php?f=4&t=470
I can't figure out how to apply rules only to subfolders.
My directory structure looks like this:
Drive/MainFolder/Folder001/Folder001a
Under the main folder, there are a lot of folders (ie. Folder001),
and under each of them, there are subfolders (ie Folder001a).
I want to apply rules only to the subfolders; Folder001a, Folder002a, etc.
Whatever I tried, the preview either showed no rules applied, or rules applied to everything under the MainFolder.
What should I do?
I can't figure out how to apply rules only to subfolders.
My directory structure looks like this:
Drive/MainFolder/Folder001/Folder001a
Under the main folder, there are a lot of folders (ie. Folder001),
and under each of them, there are subfolders (ie Folder001a).
I want to apply rules only to the subfolders; Folder001a, Folder002a, etc.
Whatever I tried, the preview either showed no rules applied, or rules applied to everything under the MainFolder.
What should I do?