Were you looking to do something like this?

http://members.shaw.ca/zekaric/gallery/200306_architecture.jpg
http://members.shaw.ca/zekaric/gallery/200312_trish.jpg

The first I did outside. I, like you, decided to take a topo and use that, exported to dxf and imported into another program to do the intersections.

The second I did entirely in Carrara 3. The only problem is that, when you convert a topo to vector, it only converts the preview representation to vector, not the final so you don't get as fine a detail as you might want. Something that annoyed me, but with clever texture mapping you may be able to fudge that.

When you extrude the boundary, make sure you close the other end and that it's a solid. Both pieces should be leak tight solids. (Ok they might not need to but from my experience with other software that does similar tasks, it's generally a good idea as the program won't be confused about what's in and out.) Also make sure that it extends completely around the outside of the other object so there is only one instersection area.

Note, Carrara usually does a good job but I've hit cases where it left some openings which you may need to patch up. This isn't a simple process for computers to do reliably even though it might sound simple in theory. There are a lot of edge cases that can cause grief and floating point precision can make a bright day very dark.