This research paper addresses the issue of developing an efficient methodology to design and manufacture a complex scaffold structure of desired porosity required for tissue engineering applications using a novel approach based on fused deposition modelling (FDM) rapid prototyping (RP) technology. The scaffold provides a temporary biomechanical structure for cell growth and proliferation to produce the required body parts. Conventional techniques of scaffold fabrication (such as fibre bonding, solvent casting and melt moulding) generate scaffolds with unpredictable pore sizes due to their limitations in flexibility and control of pore volume and distribution. Moreover, such scaffolds have poor mechanical strength and structural stability. The paper describes an FDM pre-processor that ensures the fabrication of scaffolds of desired porosity and inter-connectivity on the FDM system.