In the present study, a molecular based scheme has been developed for simulating of surface roughness and cavitation effects on nano- scale flows. In the nano-channel flows, there are some differences on the flow friction between roughness and cavitations which are not well studied. In the presented approach, based on the Molecular Dynamics Simulation (MD), the Lennard-Jones potential is used to modeling the interactions between particles. Each atom of the solid wall is anchored at its lattice site by a harmonic restoring force and its temperature has been controlled by utilizing thermostat.The roughness and cavitation have been implemented on the lower side of channel. To make a comparison between the effect of roughness and cavitation, the same dimension is used for both of them. Obtained results show, those hydrodynamic characteristics of flow and the walls shear stress depends on the roughness and cavitation sizes. The roughness on the bottom wall has more effect than cavity wall on the velocity and density profiles. Also results show that the presence of roughness on the bottom wall respectively increases the shear stress on the bottom wall and decreases its value on the top wall while, the presence of cavitation on the bottom wall has no effect on the top wall and just increase the bottom wall shear stress.