Hello jzhouaf, I recommend to use the stochastic package SARA and its Random Fields options for this task.
If you do not have SARA, trying to create such mezoscale models would require a lot of manual work and/or script or spreadsheet programming to prepare the random geometry. I definitely recommend to stay with 2D modelling. A possible solution might be to prepare a random field in a spreadsheet, and apply it to selected material properties by hand. If you send your model + some info about the problem being modelled along with your ATENA User ID (WR), we are ready to help you with the modelling in the scope of the ATENA maintenance.
Nevertheless, I suggest to contact our sales colleagues for an offer to extend your license to SARA.