Manhandling big data sets

Hoo boy. Osirix is pumping out some big data sets that prove a bit unwieldly. To explain why this is a problem let me expand on what I'm doing. Osirix is outputting an .obj file. This is 3D polygonal mesh. The higher the resolution you export it from, the finer the mesh (all trigons), the larger the file, the harder time the computer has keeping track of every poly once into the final program. To clarify, let call Osirix Step#1. We'll call the final program Step #3. Becuase Step #3, which is no stranger to polygons being a heavy duty 3D modeling program, doesn't like the number of polys being forced down it's gullet, I've resorted to using Step #2, another program that LOVES high polygon numbers, as the inbetween. One day I'll draw a flow chart. Anywho, in Step #2 you can delete polygons quickly, clean up artifacts, separate bones and generally prep things to be a little lighter when they get to Step #3. Once in Step #3, you output some really pretty images like the ones below and like this little video...