Standard Petri nets have been used to model and analyze Flexible Manufacturing Systems. The timed Petri net, which can incorporate the time delay associated with manufacturing events, provides additional information about real time behavior of practical systems. The Timed Petri Net Simulation Tool, a highly interactive graphical tool, is applied to simulate the modeled flexible manufacturing systems. Timed Petri net models are experimented with. Machine utilization data and throughput are obtained. Analysis of the results shows that the system performance can be optimized by choosing proper parameters.