A generalized surface morphology model is presented and validated to more effectively simulate the effects of surface variations (e.g., surface roughness and local thickness variations) on integrated Si photonic waveguides. To demonstrate the validity of this approach, a variety of surface roughness morphologies generated using this model are incorporated within a commercial finite-difference-time domain (FDTD) modeling package to simulate waveguide loss in Si strip optical waveguide geometries typically encountered in Si-based photonic integrated circuits. The FDTD simulation results are in very good agreement with the Payne and Lacey theoretical model for radiation-mode scattering loss based on surface correlation functions for RMS roughness values exceeding 2 to 3 nm where such scattering dominates. This agreement validates the efficacy of the generalized surface morphology model and its use for investigating the effects of irregular surface variations on photonic device performance.