The self-assembly of block copolymers BCPs proves to be a valuable method for fabricating intricate nano-patterns. Generating complex patterns with multiple morphologies, meshed structures, or variable periodicities in a single BCP system requires extra processes of surface patterning and chemical treatment. Here, a BCP system on a modulated substrate is studied to understand the effect of the underlying topography on the behavior of the top layer’s self-assembly. A self-consistent field theoretic simulation SCFT is employed to investigate the role of several key parameters including the commensurability between layers’ periodicities, the magnitude of topography height, and the chemical nature of the substrate, as well as the top surface.