A custom computer-controlled rapid prototyping system was designed and developed in this research. This system for biomanufacturing of polymer scaffolds included 3D motion control components, a nozzle, a pressure controller, and a temperature-controlled reservoir containing a biomaterial. Heating elements built into the reservoir melted the biomaterial. The pressure line attached to the reservoir provided a controllable force that extruded the polymer biomaterial through the nozzle and deposited the polymer biomaterial onto a platform to fabricate scaffolds. A low pressure (830 KPa) system was designed and fabricated to accommodate different temperatures, motion speeds, and viscosities of polymer biomaterials. The reservoir with the nozzle was mounted to servo motor-controlled linear x-y motion devices along with a third servo motorcontrolled device that controlled the z-position of the platform. Poly(ε-caprolactone) [PCL] was used to fabricate scaffolds with designed structure that were used in cell and tissue regeneration studies. 3D computer-aided design (CAD) with Pro-Engineer and computational finite element analysis (FEA) programs with MSC_Patran and MSC_Marc were used to model scaffold designs with appropriate architecture and material selection. The CAD models were used in FEA to develop new methods for determining mechanical properties of tissue scaffolds of desired structure and geometry. FEA models were validated by mechanical testing and other published results. Technology developed in this research has potential for the advancement of bio-manufacturing, and design optimization of scaffolds for tissue engineering.