In this paper, a virtual and physical prototyping approach to develop a customized implant-supported nasal prosthesis is presented. The complete workflow involves data capture, prosthesis design and prosthesis manufacturing. To design customized prostheses based on real anatomic shapes, a novel “Ear&Nose Digital Library” developed by the authors involving students of medicine and engineering in this multidisciplinary project is introduced. First, the data capture of the patient’s face is obtained by means of laser scanning, then the design and direct manufacturing of the reusable mold for the silicone processing and of the substructure for the retention of the prosthesis is carried out by means of CAD-CAM procedures and Rapid Prototyping technologies. Finally, the paper presents the discussion of the main design features that make the prosthesis a stable and reproducible system to improve maxillofacial rehabilitation of patients with facial defects.