Recent developments in tissue-engineering techniques allow physicians to treat a range of previously untreatable conditions. In the development of such techniques, scaffolds with a controllable pore size and porosity have been manufactured using solid free-form fabrication methods to investigate cell interaction effects such as cell proliferation and differentiation. In this study, we describe the fabrication of scaffolds from two types of biodegradable materials using a precision deposition system that we developed. The precision deposition system uses technology that enables the manufacture of three-dimensional (3D) microstructures. The fabrication of 3D tissue-engineering scaffolds using the precision deposition system required the combination of several technologies, including motion control, thermal control, pneumatic control and CAD/CAM software. Through the fabrication and cell interaction analysis of two kinds of scaffolds using polycaprolactone and poly-lactic-co-glycolic acid, feasibility of application to the tissue engineering of the developed SFF-based precision deposition system is demonstrated.