A generalized stochastic colored timed Petri net (GSCTPN) is used to model an IC wafer fabrication system. There are two major sub-models: a process flow model and transportation model. There are two different automated guided vehicle systems, namely, the interbay system and intrabay system. For multiple-load and variable-speed AGV systems, we embed a simple motion-planning rule and introduce a collision avoidance strategy in the model to solve the variable speed and traffic jam problems of vehicles. The simple control policies for AGV visiting and AGV routing are discussed. The heuristic rules for lot release and lot scheduling are also studied. To obtain performance measures, simulation is used. To show the promising potential of the proposed work, a real-word IC wafer fabrication system is used as a target plant layout for implementation.