Recent developments in material design and growth have resulted in photocathodes that can deliver high quantum efficiency and are sufficiently robust to use in high electric field gradient photoinjectors and free electron lasers. The growth process usually produces photoemissive material layers with rough surface profiles that lead to transverse accelerating fields and possible work function variation resulting in emittance growth. To better understand the effects of surface roughness on emitted electron beams, we have developed realistic three-dimensional models for photocathode materials with grated surface structures. They include general modeling of electron excitation due to photon absorption, charge transport and emission from rough surfaces taking into account image charge and field enhancement effects. We implemented these models in the VSim particle-in-cell code. We report results from simulations using different photocathode materials with grated and flat surfaces to investigate how controlled roughness, work function variation, and field enhancement affect emission properties.