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We report an accurate scattering loss 3-D modeling technique of sidewall roughness of optical SOI waveguides based on Fourier and finite-difference time domain (FDTD) analysis methods. The Fourier analysis method is based on the image recovery technique used in magnetic resonant imaging. Losses for waveguides with isotropic and anisotropic roughness are calculated for wavelengths ranging from 1550 to 3800 nm and compared with reported results in literature. Our simulations show excellent agreement with published experimental results and provide an accurate prediction of roughness-induced loss of 3-D arbitrary shaped optical waveguides.