The rapid prototyping (RP) technology has been advanced for various applications such as verification of design, functional test. Recently, researchers have studied various materials to fabricate functional RP parts. In this research, a nanocomposite deposition system (NCDS) was developed to fabricate three-dimensional functional parts. This system fabricates nanocomposites using photo-curable polymer resin with with various rater orientation. The NCDS is a hybrid system in which material removal process by mechanical micro-machining and/or the deposition process is combined. For multi-walled carbon nanotube (MWCNT) composites and hydroxyapatite composites, tensile strengths were tested. In addition, for MWCNT composites, the efficiency of electromagnetic-wave shielding at the frequency range of 8–12GHz was measured. From the results of tensile tests, it was confirmed that the addition of nanoparticles improved mechanical properties, and MWCNT composites revealed about 10dB electromagnetic shielding effect.