Models of 3D objects have become widely accessible in several disciplines within academia and industry, spanning from scientific visualization to entertainment. In the last few years, 3D models are often organized into digital libraries accessible over the network, and thus semantic annotation of such models becomes an important issue. A fundamental step in annotating a 3D model is to segment it into meaningful parts. In this work, we present a Java3D framework for inspecting and segmenting 3D objects represented in X3D format. In particular, we present a combination of segmentation and merging techniques for producing a feasible decomposition of the boundary of a 3D object. We represent such decomposition as a graph, that we call the segmentation graph which is the basis for semantic annotation. We describe also the interface we have developed to allow visualization and browsing of both the decomposition and the segmentation graph in order to understand the topological structure of the resulting decomposition.