You can try material studio to see the adsorption and for constructing the surface. I am not aware about the cutting the surface at diff angle/planes. If you want to use it you can check in its tutorial. They have explained every thing.

with regards

raeesh

yes, you can construct with structure reference

Not matter how you prepare the structure. Correct force field is essential for your further simulation. If similar research has been done, you may check how they did that. If not, it's hard to choose proper force field to proof the correctness.