I've just discovered that Profantasy has an add-on for Campaign Cartographer called Perspectives that does isometric stuff
Turning a 2D map into isometric is no big deal (rotate and scale), but extruding the flat elements is quite intriguing, how does the vertical part looks like?
BTW, if you are ready to put some work into it to have a really good result, you can turn simple 3D paper models parts (certainly walls and floors) into isometric elements. On "normal isometric, it would just be a 30° skew. On the kind of isometric used by Maptool, it would just be a little more difficult.