Collisions and Intersections?

I am printing with a Replicator 2 and using Makerbot Software to slice and export with. As I work my way into my own models I am using Blender to do my 3D modeling. I have noticed that anytime a collision between two surfaces that Makerbot tries to make a cut-line at the edge. I assume this is for printing items that are meant to print together but then they will move separately after printing.
In this example the ball and cube on the left is at total intersection and you can see the small gap the the software left. The second ball was cut to match the surface of the cube and it was then snapped to the surface and so was the cylinder on the far right.
I want to be able to just smash surfaces into each other and have them print as one.
Any suggestions?
Attachment 7515

use openscad :-)
It only makes solid models.

That is not a bad suggestion Curious Ardvark but too late in the game to change on this project. I was hoping more for a possible profile change so that the slicer does not get confused like on this head print. The eyes were a separate element inside of the head sculpt so the printer decided to print the eyes and not the cheeks.
Attachment 7526