You can disable the archiving of top-level folders or subfolders (or both) in the retention folder hierarchy for an FSA target by unchecking the appropriate Archiving boxes in the FSA target properties.
To disable archiving of some or all retention folders on an FSA target
In the Administration Console, expand the site and click Targets > File server.
Expand the relevant file server and select the volume that contains the target folder.
Right-click the target folder whose properties you want to change, and select Properties.
For example, if you select only Archive subfolders in Retention Folder hierarchy, the top-level folders are not archived but all subfolders are archived.