Vertically oriented materials, such as van der Waals heterostructures, which have novel hybrid properties, are crucial for fundamental scientific research and the design of new nano-devices. Currently, most available theoretical methods require applying a supercell approach with periodic boundary conditions to explore the electronic properties of such nanomaterials. Herein, we present supercell-core software, which provides a way to determine the supercell of non-commensurate lattices, in particular van der Waals heterostructures. Although this approach is very common, most of the reported work still uses supercells that are constructed “by hand” and on a temporary basis. The developed software is designed to facilitate finding and constructing optimized supercells (i.e., with small size and minimal strain accumulation in adjacent layers) of vertically stacked lattices. The developed software tool is accessible as open-source free software.