Because 3-D data are acquired using 3-D sensing such as stereo vision and laser range finders, they have inhomogeneous and anisotropic noise. This paper studies optimal computation of the similarity (rotation, translation, and scale change) of such 3-D data. We first point out that the Gauss-Newton and the Gauss-Helmert methods, regarded as different techniques, have similar structures. We then combine them to define what we call the modified Gauss-Helmert method and do stereo vision simulation to show that it is superior to either of the two in convergence performance. Finally, we show an application to real GPS geodetic data and point out that the widely used homogeneous and isotropic noise model is insufficient and that GPS geodetic data are prone to numerical problems.