||Finite Element Method (FEM) provides a powerful tool to study mechanical behavior of prostheses as well as prosthesis design, yet in most cases of long bone, approximated models are applied for the job. Better results demand more accurate description of the model. In this practice, a system is designed and implemented to reconstruct a 3 dimensional model of bones from computer tomographical (CT) images with direct interfacing facility with other CAD and Finite Element Analysis systems. Several practical schemes of 3D reconstruction are discussed and implemented. Experiments were performed on both synthetic and real CT images to evaluate the system. The bone model together with the prosthetic interface model, which can also be created from the system upon preprocessing of the bone cross-sectional images, is then analyzed the using Finite Element method. Optimized prosthetic structures are introduced upon analytical results. FE analyses of the optimized designs are practiced. The tibia of a goat is taken as the subject of study; the whole process as well as the results is intended to be referred to as an explorative fulfillment for prosthesis structure analysis and design.