What is the best 3D modelling software for designing a heterogeneous composite material. 

  It is easy to deign a homogeneous 3D model of composite for an structural analysis. 3D models created using SOLID WORKS, CREO etc., are homogeneous models, even 3D models created using powerful FEM packages like ANSYS and ABAQUS are homogeneous possessing homogeneous structural property. What is the best software for creating a heterogeneous composite structure for structural analysis.

If you are interested in the microstructure of composites and its effects on permeability, stiffness, etc. etc. it may also be worth taking a look at the GeoDict software at https://www.geodict.com. You will find many publications that use the software in the Showroom -> Scientific publications using GeoDict, Topic Composites section of the web site.