Scaffolds composed of biodegradable polymers and biocompatible ceramics are being used as substitutes for tissue engineering. In the development of such techniques, scaffolds with a controllable pore size and porosity were manufactured using solid free-form fabrication (SFF) methods to investigate the effects of cell interactions such as cell proliferation and differentiation. In this study, we describe the adhesion of human bone marrow stromal cells (hBMSCs) and proliferation characteristics of various scaffolds, which consist of biodegradable materials, fabricated using a multi-head deposition system (MHDS) that we developed. The MHDS uses novel technology that enables the production of three-dimensional (3D) microstructures. Fabrication of 3D tissue engineering scaffolds using the MHDS requires the combination of several technologies, such as motion control, thermal control, pneumatic control and computer-aided design/computer-assisted manufacturing software. The effects of a polymer and ceramic on a tissue scaffold were evaluated through mechanical testing and cell interaction analysis of various kinds of scaffolds fabricated using polycaprolactone, poly-lactic-co-glycolic acid and tri-calcium phosphate for bone regeneration applications. Based on these results, the feasibility of application to the tissue engineering of SFF-based 3D scaffolds fabricated by the MHDS was demonstrated.