Recent developments in shape-based modeling and data acquisition have brought three-dimensional models to the forefront of computer graphics and visualization research. New data acquisition methods are producing large numbers of models in a variety of fields. Three-dimensional shape-based matching and registration (alignment) are key to the useful application of such models in areas from automated surface inspection to cancer detection and surgery. The three-dimensional models in these applications are typically huge. State-of-the-art simulations in computational fluid dynamics produce upward of four terabytes of data per second of flow. Research-level magnetic resonance imaging (MRI) resolutions can reach 1 cubic micro-meter. As a result, object registration and matching algorithms must handle very large amounts of data.The algorithms developed in this thesis accomplish automatic registration and matching of three-dimensional voxelized models. We employ features in a wavelet transform domain to accomplish registration. The features are extracted in a multiresolutional format, thus delineating features at various scales for robust and rapid matching. Registration is achieved through seeking peaks in sets of rotation quaternions using a voting scheme, then separately identifying translation. The method is robust to occlusion, clutter and noise. The efficacy of the algorithm is demonstrated through examples from solid modeling and medical imaging applications.