Traditionally, industrial sheet metal forming technologies use rigid metallic tools to plastically deform the blanks. In order to reduce the tooling costs, rubber or flexible tools can be used together with one rigid (metallic) die or punch, in order to enforce a predictable and repeatable geometry of the stamped parts. If the complete tooling setup is built with deformable tools, the final part quality and geometry are hardly predictable and only a prototypal production is generally possible. The aim of this paper is to present the development of an automatic tool design procedure, based on the explicit FEM simulation of a stamping process, coupled to a geometrical tool compensation algorithm. The FEM simulation model has been first validated by comparing the experiments done at different levels of the process parameters. After the experimental validation of the FEM model, a compensation algorithm has been implemented for reducing the error between the simulated component and the designed one. The tooling setup is made of machined thermoset polyurethane (PUR) punch, die, and blank holder, for the deep drawing of an aluminum part. With respect to conventional steel dies, the plastic tools used in the test case are significantly more economic. The proposed procedure is iterative. It allows, already after the first iteration, to reduce the geometrical deviation between the actual stamped part and the designed geometry. This methodology represents one step toward the transformation of the investigated process from a prototyping technique into an industrial process for small and medium batch sizes.