A computer-aided design method for modifying the mechanical structure of electro-mechanical systems, eg. robots and positioning systems, is presented in this paper. The pole-zero locations and other system characteristics are represented in relation to the structural geometry by using a finite element method. The inverse problem of determining a geometry which will yield better dynamic characteristics is formulated and solved. Based on sensitivity analysis and the singular value decomposition of the sensitivity matrix, useful information is provided to the designer for making effective design changes and understanding trade-offs among multiple system characteristics to be improved. This decomposition also provides us with a new type of geometric design mode-shapes that characterizes all possible design changes affecting system characteristics. The design methodology is implemented to develop a computer-aided structure modification system. A design example of a flexible robot arm demonstrates the usefulness of the system.