Abstract: This paper introduces a novel technique for joint surface reconstruction and registration. Given a set of roughly aligned noisy point clouds, it outputs a noise-free and watertight solid model. The basic idea of the new technique is to reconstruct a prototype surface at increasing resolution levels, according to the registration accuracy obtained so far, and to register all parts with this surface. We derive a non-linear optimization problem from a Bayesian formulation of the joint estimation problem. The prototype surface is represented as a partition of unity implicit surface, which is constructed from piecewise quadratic functions defined on octree cells and blended together using B-spline basis functions, allowing the representation of objects with arbitrary topology with high accuracy. We apply the new technique to a set of standard data sets as well as especially challenging real-world cases. In practice, the novel prototype surface based joint reconstruction-registration algorithm avoids typical convergence problems in registering noisy range scans and substantially improves the accuracy of the final output.