In the digital age of medicine, patient-specific 3D anatomical reconstructions are becoming increasingly relevant in several applications, starting from bio-mechanical simulation, virtual surgery, implant design to computer-assisted diagnosis. While problems related to imaging and 3D reconstruction have been largely resolved by the advancement in technologies, tools for extracting, coding, sharing and retrieving the semantic content of the patient-specific 3D models are still far from being satisfactory. In this context, we propose SemAnatomy3D framework that aims to bridge the semantic gap between patient-specific 3D geometry and formalized domain knowledge for making the semantics more usable for the definition of patient-specific atlas of anatomy. The purpose of this paper is to describe primary components of the framework. We specialized our framework for the carpal region, but, in principle, it can support similar tasks for other anatomical districts.