System inference, i.e., the building of system structure from system behavior, is widely recognized as a critical challenging issue. In System Theory, structure and behavior are at the extreme sides of the hierarchy that defines knowledge about the system. System inference is known as climbing the hierarchy from less to more knowledge. In addition, it is possible only under justifying conditions. In this paper, a new system inference method is proposed. The proposed method extends the process mining technique to extract knowledge from data and to represent complex systems. The modularity, frequency and timing aspects can be extracted from the data. They are integrated together to construct the Fuzzy Discrete Event System Specification (Fuzzy-DEVS) model. The proposed approach consists of three stages: (1) extraction of event logs from data by using the System Entity Structure method; (2) discovery of a transition system, using process discovery techniques; (3) integration of fuzzy methods to automatically generate a Fuzzy-DEVS model from the transition system. The last stage is implemented as a plugin in the Process Mining Framework (ProM) environment. A case study is presented in which Fuzzy-DEVS model is inferred from real life data, and the SimStudio tool is used for its simulation.