The scaffold serves as 3D substrate for the cells adhesion and mechanical support for the newly grown tissue by maintaining the 3D structure for the regeneration of tissue and organ. In this paper, we proposed integrated scaffold fabrication system using multi-axis rapid prototyping (RP) technology. It can fabricate various types of scaffolds: arbitrary sculptured shape, primitive shape, and tube shape scaffolds by layered dispensing biocompatible/ biodegradable polymer strands in designated patterns. In order to fabricate the 3D scaffold, we need to generate the plotting path way for the scaffold fabrication system. We design a data processing program - scaffold plotting software, which can convert the 3D STL file, primitive and tube model images into the NC code for the system. Finally, we fabricated the customized 3D scaffolds with high accuracy using the plotting software and the fabrication system.