The microelectronic industry has moved from matured bulk planar transistor to three-dimensional (3D) architectures with small non-trivial cross-sections and short channel lengths requiring quantum simulation techniques. In addition, novel materials, which enhance the transistor performance, are considered as silicon channel replacement. This necessitates the efficient inclusion of surface roughness scattering in quantum transport simulations. In this work, we report an approximate methodology to include surface roughness scattering in 3D Non-Equilibrium Green's Function (NEGF) simulations using self-energy formulation within the self-consistent Born approximation (SCBA). The method is validated with the well established methodology of treating surface roughness as a variability source. We also extract the mobility from our simulations and then compare with to those reported in the literature. © 2019 IEEE.