The purpose of this study is to clarify the mechanical behavior of human lumbar vertebrae (L3/L4) with and without fusion bone under physiological axial compression. The author has developed the program code to build the patient specific three-dimensional geometric model from the computed tomography (CT) images. The developed three-dimensional model provides the necessary information to the physicians and surgeons to visually interact with the model and if needed, plan the way of surgery in advance. The processed data of the model is versatile and compatible with the commercial computer aided design (CAD), finite element analysis (FEA) software and rapid prototyping technology. The actual physical model is manufactured using rapid prototyping technique to confirm the executable competence of the processed data from the developed program code. The patient specific model of L3/L4 vertebrae is analyzed under compressive loading condition by the FEA approach. By varying the spacer position and fusion bone with and without pedicle instrumentation, simulations were carried out to find the increasing axial stiffness so as to ensure the success of fusion technique. The finding was helpful in positioning the fusion bone graft and to predict the mechanical stress and deformation of body organ indicating the critical section.