In recent years, digital content of three-dimensional (3D) scientific objects has become widespread and is made available in a plethora of on-line scientific repositories. A systematic and formal approach becomes necessary to represent the knowledge/information related to these objects, in order to facilitate their search, retrieval and reuse. In this paper, we employ semantic interoperability to manage 3D scientific object content in a large-scale framework of scientific applications that consists of 3D shape models, associated tools and resources. We use an advanced ontological organization for their metadata, powerful reasoning engines for their search and retrieval and we elucidate several crucial issues in the design and implementation of 3D knowledge-based management systems.