I was having some trouble getting the top section of Darthwahl's Floating Lighthouse Island (http://www.thingiverse.com/thing:23519/) to print. When I looked at the makerware slicer output, I saw gaps in the lighthouse/house. Evidently some of the surfaces didn't plot well in makerware.

I imported the file into tinkercad, subtracted it from an arbitrary cubic volume, then subtracted that volume from another arbitrary cubic volume. The end result looks identical, but sliced well in makerware, with no floating lighthouse parts.