In recent years, flexible manufacturing system as a response to market demands has been proposed to increase product diversity, optimum utilization of machines andperiods of short-term products. The development of Computer systems has provided the ability to build machines with high functionality and the necessary flexibility to perform various operations. However, due to the complexity and the random nature of these problems, deterministic algorithms are not highly accurate andefficient enough. In this paper, Computer simulation models are used to optimize flexible manufacturing system FMS). The objectives of this paper are included: the optimal time served in each unit, the optimal number of servers in each unit, and the optimum number of domestic transportation fleet based on type. At the first step, source-destination traffic matrix is presented for development, including: service time and traffic volume are used. The computational results show the accuracy and efficiency of using simulation tools in these problems.