The objective of this paper is to present a methodology for design of the FMS by using a new modeling tool which is called SE&TPN(Safe Extended & Timed Petri Net). A FMS, which consists of various machine groups, may produce machine parts in different physical dimensions and lot size. The approach involves the SE&TPN modeling by Petri-nets. The proposed algorithm can handle determining of firing count vector by incidence matrix and adjustment of conflict using the marking of SE&TPN. The SE&TPN is defined as nets that can have at most one token in one place and can have elements such as permissive arcs and inhibitor arcs in addition to elements. The SE&TPN with permissive arcs and inhibitor arcs are intuitively direct approach to increase the modeling power of the SE&TPN. Finally, this paper is to develop a modulation to optimize the system problems of FMS using SE&TPN which describes exactly features of Petri Nets.