The paper examines the Third Mission of universities from the point of view of company collaboration in the prototype development process. The paper presents an implementation of university-enterprise collaboration in prototype development described by means of process modeling notation. In this article, the focus is on modeling the software prototyping process in a research context. This research paper introduces prototype development in a university environment. The prototypes are made in collaboration with companies, which offered real-world use cases. The prototype development process is introduced by a modeling procedure with four example prototype cases. The research method used is an eight-step process modeling approach. The goal was to find instances of activity, artifact, resource, and role. The results of modeling are presented using textual and graphical notation. This paper describes the data elicitation, where the process knowledge is collected using stickers-on-the-wall technique, and the creation of the model is described. Finally, the shortcomings found in our existing practices and possibilities for improving our prototype development processes and practices are discussed.