Dear Sajjad Sattari, Prof. Dierk Raabe gives enough full remarks to your question. I think that 3D FEM modelling of fine structure of materials such as nanocomposites requires too much computer cost. The analytic methods of micromechanics and multilevel (hybrid) models are seemed more effective than pure FEM simulation (see, f.e.,  "Mesomechanical analysis of polymer composites reinforced by short fibers with taking into account an interphase layer // Mechanics of Composite Materials, 2012, Vol. 48, N 2, P. 171–178.

Nevertheless, ABAQUS, ANSYS and so may be used for detailed description of stress-strain state of local fragments of composites.

Good luck!

Thank you very much, dear Raabe

Thank you very much, dear Shilko