A so-called “Design Process Investigation toolbox” (DPI toolbox), has been developed. It is a set of computational tools that simulate spatial-structural design processes. Its objectives are to study spatial-structural design processes and to support the involved actors. Two case-studies are presented which demonstrate how to: (1) study the influence of transformation methods on design instances and (2) study the influence of transformation methods on the behavior of other transformation methods. It was found that in design instances with the same type of structural elements the influence of a specifically varied transformation method is more explicit; while, when different types are present this influence is more undetermined. It was also found that the use of two specifically different structural modification methods have little influence on the sub-sequential spatial transformation method.