Chemoepitaxy is often used to induce pattern density multiplication in the directed self-assembly (DSA) of block copolymers (BCPs) by using a chemically patterned guiding underlayer. This underlayer is often viewed as being a flat underlayer composed of a pinning stripe region and a neutral stripe region, where the pinning stripe is a region highly preferential to one phase of the BCP and the neutral stripe is a region that is slightly preferential to the other phase of the BCP that is not attracted by the pinning stripe. However, in producing these chemoepitaxial patterns, it is likely that unexpected topography might be introduced into the system, which may adversely affect the ability for the underlayer to guide the phase separation of the BCP film, and may deform any resulting lamellae. The current work presented in this paper explores the effect that topography in these chemoepitaxial underlayers has on the alignment of the BCP film. These underlayer effects have been evaluated using detailed mesoscale molecular dynamics simulations.