Development of control model and system for FMS (Flexible Manufacturing Systems) has long been interested by researchers. Presented in the paper is method for performance evaluation of FMS by using a new modeling tool which is called SE&TPN(Safe Extended & Timed Petri Net). So, the procedure of modeling in the FMS is based on the IOM (Integrated Object-oriented Modeling) paradigm The purpose of this p a p is to develop a modularzation to optimize the system problems of FMS using SE&TPN which describes exactly features of DES(Discrete Event System). Finally, the algorithm is developed using the developed method for a design technique of DES. So, we propose in this paper a construction matrix suitable for DES, which represents the marking change that is the dynamic behaviors.