Stress topology optimization with Millipede

Hi!

I am having some issues with a stress topology optimization of a Kangaroo found shape. I am using Millipede for the first time and the task is to create a pavilion using a form finding tool and then optimize that structure.

My first plan was to optimize the whole shell using Milipede 3D optimization, but I can only make that work for a complete square plate - not for my structure.

Now I am aming at optimizing small parts of it using the technique used in this http://ming3d.com/DAAP/ARCH4002sp2015/?p=435 

But I can't figure out how to perfrom the operation on my structure.

Can you help me? Don't mind the Karamba components :)