David,
The Create File List and FileSet Task/Commands do just that, create (Including/Excluding)
Files from a Folder. Under the rules of Include/Exclude, a folder is only "Excluded" if no files exists in the folder matching the desired pattern.
To Exclude a folder (regardless of file names) you would need to do an "Exclude *.*"
Otherwise, there is a Tips and Tricks Email that I sent out recently explaining how to perform (Project code included) a Folder Selection that might help you in this endeavor. It can be found at the following link:
Working with Folders
Your only other option is to retrieve the file list (including the folder you do not want to process) and then looping through that FileList with your first statement inside the loop being :
<iterateLoop condition="${ contains( '\MyFolderName\', false )}
That way you process what you're needing, then remove the folders you do not want to process.