Organise Format Factory output?

I have just used FF for audio and it was lightning fast!

I select a Folder, I ask for Entire Tree and it then picks up the folder's WAV files for conversion. Unfortunately it then combines that folder and any others I chose into a single stream of output files, with no organisation into albums or artists. I will need that if I place the output on SD card for playing.

Is there a way to get FF to set the output like this?

EDIT: I have just tried actually asking to do the entire parent folder, hoping that this would trigger the files being placed in their respective sub-folders, but they all just streamed to my chosen output folder.

Thanks for any help.

Nick

 

Firefox? I am asking about format factory.