The nanofluidics is characterized by a large surface-to-volume ratio, so that the surface properties strongly affect the flow resistance. We present here the results showing that the effect of wetting properties and the surface roughness may considerably reduce the friction of fluid past the boundaries. For a simple fluid flowing over hydrophilic and hydrophobic surfaces, the influences of surface roughness are investigated by the nonequilibrium molecular dynamics (NEMD) simulations. The fluid slip at near a solid surface highly depends on the wall-fluid interaction. For hydrophobic surfaces, apparent fluid slips are observed on smooth and rough surfaces. The solid wall is modeled as a rough atomic sinusoidal wall. The effects on the boundary condition of the roughness characteristics are given by the period and amplitude of the sinusoidal wall. It was found that the slip velocity for wetting conditions at interface decreases with increasing effects of surface roughness. The results show the surface rougheness and wettability determines the slip or no-slip boundary conditions. The surface roughness geometry shows significant effects on the boundary conditions at the interface.