Maptool is capable of using a tile-based approach to mapping, but you'll need to find the resources. Check around in the Mapping Elements section; I know there are a few threads in there with tiles you can use, and Torstan made a set of map objects that can be used to build dungeons of any size and shape. Also, there was a mapping challenge a while back that resulted in several sets of tiles, so look back through the challenges forum too.

That said, Maptool isn't really so much a map-making tool as it is a game interface. It can certainly be used to build the maps, if you have the tiles, but there are other programs that might do it better. Dungeonforge comes to mind—I think it's a tile-based mapper, but I've never used it, so I'm not sure.