A difficult problem in operating Flexible Manufacturing Systems (FMS) is to control the system in real-time by coordinating heterogeneous machines and integrating distributed information. The objective of the paper is to present the models and methodologies useful to resolve the difficult problem. The detailed objectives can be described in three folds. First, a hierarchical Colored and Timed Petri-Net (CTPN) is designed to control an FMS in real-time. The concerned FMS consists of a loading station, several machining cells, a material handling system, and an unloading station. Timed-transitions are used to represent the timed-events such as AGV movements between stations and cells, part machining activities in the cells. Signal places are also used to represent communication status between the host and the cell controllers. To resolve the event conflicts and scheduling problems, dispatching rules are introduced and applied. Second, an implementation methodology used to monitor and diagnose the errors occurring on the machines during system operation is proposed. Third, a Petri-Net simulator is developed to experiment with the designed control logic.