Structured light illumination systems can measure a target’s two-dimensional height profile. Recent advancements in computational power and algorithms have enabled the predesign of optical systems where all experimental variables are determined prior to use in the laboratory. We present a predesign process to align the projector of a custom-structured light illumination system. The predesign method uses the native optical design file to simulate the residual aberrations and can perform a trade space analysis to tailor the alignment variables to desired preferences. The presented method can predict the experimental focus position to 1.6 μm root mean square over a broad range of physical settings.