Coherence scanning interferometry (CSI), a type of interference microscopy, has found broad applications in the advanced manufacturing industry, providing high-accuracy surface topography measurement. Enhancement of the metrological capability of CSI for complex surfaces, such as those featuring high slopes and spatial frequencies and high aspect-ratio structures, requires advances in modeling of CSI. However, current linear CSI models relying on approximate surface scattering models cannot accurately predict the instrument response for surfaces with complex geometries that cause multiple scattering. A boundary elements method is used as a rigorous scattering model to calculate the scattered field at a distant boundary. Then, the CSI signal is calculated by considering the holographic recording and reconstruction of the scattered field. Through this approach, the optical response of a CSI system can be predicted for almost any arbitrary surface geometry.