I use a * to list all the files in the my multi-emulator set-up for Mamewah.
It lists all my files and shortcuts, but not the folders.  
You could create shortcuts (or any file with iso name) in the rom folder and then launch a bat file from Mamewah such as
SegaCD.bat  that includes:
      gens c:\roms\%1\%1.iso  
Just make sure Memewah does not send rom path or extension.
If I had an ISO i would try this oput for you but it seems like it shoudl work.
-wj2k3