The tutorial of "Building a Si-Si3N4 interface" is of course demonstrated for the two bulk materials, their surface structures (e.g., thin films), their interface, and their device structures.
The tutorial of "Opening a band gap in silicene and bilayer graphene with an electric field" is demonstrated for a very thin film of silicon or graphite. I guess that your problem is how to build a thin film of beta cristobalite. This can be done by the "Cleave" tool in VNL. See one of steps in the tutorial of "Building a Si-Si3N4 interface".