The Official M&L3 Ripping Project *WARNING CONTAINS SPOILERS*

[puggsoy]

So far as we know hard-ripping and editing out the backgrounds is the only way, at least until Yoshi Magic manages to support it (if that ever happens). Tile Molester might work but if it does it mustn't be worth the effort if Ridge is hard-ripping Bowser. If it were then I'm sure they'd already be done.

If you do plan to attempt to rip Mario, my Background Remover app (which you can get here) might help somewhat.