Automated process discovery algorithms aim to automatically create process models based on event data that is captured during the execution of business processes. These algorithms usually tend to use all of the event data to discover a process model. Using all (i.e., less common) behavior may lead to discover imprecise and/or complex process models that may conceal important information of processes. In this paper, we introduce a new incremental prototype selection algorithm based on the clustering of process instances to address this problem. The method iteratively computes a unique process model from a different set of selected prototypes that are representative of whole event data and stops when conformance metrics decrease. This method has been implemented using both ProM and RapidProM. We applied the proposed method on several real event datasets with state-of-the-art process discovery algorithms. Results show that using the proposed method leads to improve the general quality of discovered process models.