You can use Location clauses in the filter, as described here.
Note that the SubFolder clauses described there do not work with the Synchronize tool. You have to use Location clauses (also described there).
The Synchronize tool only considers files, never folders, so the filter is only applied to each file to decide whether or not to copy the file. (If a file is in a nested folder then the folder will be copied implicitly.)
If you don't care about seeing what will be synchronized before you commit to the sync, you may find that the Copy UPDATEALL command works better. That can be given a filter which may use SubFolder clauses to include/exclude certain folders.