A FMS is a typical discrete event system exhibiting concurrency, asynchronicity and non-determinism. To represent a FMS with those characteristics, Colored and Timed Petri Nets is defined and the modeling procedure is provided in this paper. To analyze and evaluate the performance of a FMS, a simulation software is developed and applied to SNU FMS/CM Center. This software enables to detect the bottleneck machine and decide the optimal direction in case of the expansion of a FMS.