Create graphene layers with STL file

Hello everyone.
I want to create graphene layers by Materials Studio and then cut an atomic system, using a 3-D shape defined in an STL file by using Atomsk (follow this tutorial Atomsk - Tutorial - Using 3-D Models in STL format 1). Then I import this atomic system into Material Studio
Could you help how to cut an atomic system of graphene layers, using a 3-D shape defined in an STL file and then import into Material Studio?

Thank you very much.