Surface registration plays a fundamental role in many applications in computer vision and aims at finding a oneto-one correspondence between surfaces. Conformal mapping based surface registration methods conformally map 2D/3D surfaces onto 2D canonical domains and perform the matching on the 2D plane. This registration framework reduces dimensionality, and the result is intrinsic to Riemannian metric and invariant under isometric deformation. However, conformal mapping will be affected by inconsistent boundaries and non-isometric deformations of surfaces. In this work, we quantify the effects of boundary variation and non-isometric deformation to conformal mappings, and give the theoretical upper bounds for the distortions of conformal mappings under these two factors. Besides giving the thorough theoretical proofs of the theorems, we verified them by concrete experiments using 3D human facial scans with dynamic expressions and varying boundaries. Furthermore, we used the distortion estimates for reducing search range in feature matching of surface registration applications. The experimental results are consistent with the theoretical predictions and also demonstrate the performance improvements in feature tracking.