In this paper, we describe a novel method for searching and comparing 3D objects. The method encodes the geometric and topological information in the form of a skeletal graph and uses graph matching techniques to match the skeletons and to compare them. The skeletal graphs can be manually annotated to refine or restructure the search. This helps in choosing between a topological similarity and a geometric (shape) similarity. A feature of skeletal matching is the ability to perform part-matching, and its inherent intuitiveness, which helps in defining the search and in visualizing the results. Also, the matching results, which are presented in a per-node basis can be used for driving a number of registration algorithms, most of which require a good initial guess to perform registration. In this paper, we also describe a visualization tool to aid in the selection and specification of the matched objects.