Abstract The methodological procedure for generating three-dimensional (3-D) finite element analysis (FEA) geometry models from CT or MRI medical imaging scan data was developed in this study. Medical images of a human scapula and a fifth proximal phalangeal bone were used to demonstrate the techniques of image processing and generation of 3-D FEA models. The biomedical imaging quality and its effects on the outcome of the FEA geometry model was also studied.