This paper illustrates a systematical surface topography measurement and evaluation method based on a 3D optical system. Firstly, the point cloud data of the workpiece are extracted by the use of a 3D structured light measurement system, and the STEP file of the design model is converted into point cloud data. Secondly, the local measurement point cloud (LMPC) and digital model point cloud (DMPC) are registered by a multivariate local descriptor registration scheme proposed in this study. Thirdly, the surface shapes extracted from the STEP file are applied as a reference to segment the measuring point cloud. Finally, an error analysis scheme is conducted on specific functional surfaces. An experiment was conducted to analyse the flatness, cylindricity and roughness to demonstrate the effectiveness and advantage of the method. The comparison results show that the proposed method outperforms other 3D optical surface topography analysis methods.