Hello Danish,

To my knowledge, you listed most of the available open-source tools used by colleagues currently doing 3D microstrucutres modeling.

I heard (and Googled) about this one :

http://matforge.org/cmu/wiki/mmsp

But never used it...

Off3D might do the job. 

 http://www.ctcms.nist.gov/oof/oof3d/