Tissue engineering scaffolds with intricate and controlled internal structure can be realized using computer-aided design (CAD) and layer manufacturing (LM) techniques. Design and manufacturing of scaffolds for load-bearing bone sites should consider appropriate biocompatibile materials with interconnected porosity, surface properties, and sufficient mechanical properties that match the surrounding bone, in order to provide adequate support, and to mimic the physiological stress-strain state so as to stimulate new tissue growth. The authors have previously published methods for estimating subject- and site-specific bone modulus using computed tomography (CT) data, CAD, and process planning for LM of controlled porous scaffolds. This study evaluates the mechanical performance of the designed porous hydroxyapite scaffolds in load-bearing sites using a finite element (FE) approach. A subject-specific FE analysis using femoral, defect site geometry and anisotropic material assignment based on CT data is employed. Mechanical behaviour of the femur with scaffold in stance-phase gait loading, which has been shown experimentally to produce clinically relevant results, is analysed. The comparison of results with simulation of healthy femur shows an overall correspondence in stress and strain state which will provide optimized mechanical properties for avoiding stress shielding, and adequate strength to avoid failure risk and for active bone tissue regeneration.