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The construction of engineered bone mostly focuses on simulating the extracellular matrix (ECM) for proper biological activity. However, the complexity of architecture and the variability of the mechanical properties of natural bones are related to individual differences in age, nutritional state, mechanical loading and disease status. Defect substitutions should be normed with the host natural bone, balancing architectural and mechanical adaption, as well as biological activity. Using a freeform fabrication (FFF) method, we prepared polycaprolactone (PCL) scaffolds with different architectures. With simulation of structural and mechanical parameters of rabbit femur cancellous bone, individual defect substitution with the characteristics of the rabbit femur was obtained with high porosity and connectivity. Biological adaption in vitro was examined and osteoid formation in vivo was assessed by implantation in situ. Simulating the femur cancellous bone, 300-μm FFF PCL scaffolds had better architectural and mechanical properties. The protocol produced an architecturally, mechanically and biologically adaptive construction of an individual model for rapid-prototype PCL scaffolds. A guide system was developed to accurately reproduce virtually individual defect substitutions of the bone.