In building structure design, refinements during construction for practical use or space conflicts induce construction delays and budget increases. Building information modeling (BIM) provides a 3D building model which includes the structure’s size, material, and construction information so designers clearly understand the whole construction process. For an irregular shaped building or elements such as a ramp or a curved roof, space conflict problems occur. The Autodesk’s Navisworks program provides a visual analysis tool for users to roam in a 3D model to simulate possible space conflicts and avoid them before the final design. In this study, we used the AutoDesk Revit program to set up a building system with a Navisworks space distance measurement tool to confirm the design’s rationality. An optimal structure system design process is proposed for practical applications to reduce the possibility of design changes.