Since the emergence of tissue engineering (TE), numerous researchers, particularly in the areas of materials, biological science, and engineering, have aimed to provide viable substitutes for the repair and regeneration of musculoskeletal and organ tissues. Bone TE has been extensively explored to mimic the anatomical geometry of bone with varied pore size distribution and varying mechanical properties in a radial direction (a functional gradient). This TE approach was explored to promote faster functional recovery of defective bones due to congenital, traumatic, or degenerative reasons. The present study integrated an appropriate additive manufacturing or rapid prototyping technique with automated computer-aided design models. This process was applied to the manufacture of a functionally graded scaffold (FGS). The FGS system takes into consideration both microscale anatomical geometries and mechanical properties of the native bone via an established porosity-stiffness relationship. Experimental verification of the FGS model was carried out by the fabrication of a femur bone segment using a selective laser sintering system. The physical femur model demonstrated good replication of the FGS structure that was generated. Future work aims to implement the FGS system for other musculoskeletal and organ tissues and integrate the current work with the authors’ in-house developed “computer aided system for tissue scaffolds” or CASTS system.