Design process of a machine tool is sometimes experience basis and time-consuming. The author has proposed a design tool for machine tools based on form-shaping theory and robust design technique. The tool can determine suitable configuration of machine tools, or important design parameters and error factors that affect machine tool performance, without prototyping. Especially in case of recently popular 5-axis machine tools, since the number of motion axis increases, there are huge options of axes combinations. It is difficult for machine tool designers to simulate the performance of every design option. Contrarily, the proposed design tool can clarify which design option of machine tool have better performance. In this paper, the tool is applied to the design of 5-axis machine tools. It enables to narrow the selection and make the design procedure more efficient. It also tries to suggest where the rotational motion axes should be placed. Finally, it is concluded that the design tool is effective in supporting configuration design of 5-axis machine tools structure where design knowledge has not been completely established.