Are you perhaps confusing The After Years with some other FF WiiWare game, Trop? I don't see why it would be impossible. I don't know what method was used to map Mega Man 9 or 10 (sounds like a WiiWare emulator), so couldn't the same method be used?
Plus, at least as far as I could tell from playing just the first chapter of the After Years, it looks like it uses the same tileset as Final Fantasy II/IV on the Super NES. Many of the areas are probably mostly the same. If we had more Final Fantasy IV maps (sheesh, VGMaps.com needs more Final Fantasy maps overall), it could be as easy or maybe easier to edit those maps to recreate the new ones rather than trying to rip them directly.