A molecular dynamics simulation is used to investigate the effect of surface roughness on the nano-rheology of ultra-thin films confined between two solid walls. The results show that friction is sensitive to the confining surface morphology and the fluid molecules near the two confining surfaces are in a layering solid-like structure. At a high shear rate, the interfacial layers of the film stick to the walls, resulting in partial slip inside the film and the development of shear stress in the viscous molecular fluid. The frictional resisting force is due to the shear in the viscous molecular fluid but not dependent on the critical yield stress of the solid-like structure as in the case of smooth boundaries.