Just wanted to offer one other suggestion:
A new 3D modeller called Modo.
It was made by programmers who worked on Lightwave and is superior to other modellers in some areas (not to mention being much more enjoyable to use
).
http://www.luxology.com/
You can download the program for free to try out till you are ready to buy it (if you decide to).
You could also see if any of these videos hint at what you need:
http://www.luxology.com/training/?mode=Category&id=2
Also, since so many aspects of the program can be automated, maybe the particular problem you have could be automated to some extent using this program.
See this video, if you want to see what I mean:
http://www.luxology.com/training/video.aspx?id=83
Maybe this would allow you to "script" your solution.