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With the emerging of highly automated and flexible manufacturing systems in semiconductor fabrication, reliability and optimal productivity of such systems require very intelligent and complex control systems. Deadlock issue arises easily in these systems due to shared equipment usage and high production flexibility. This paper extends the event-based deadlock avoidance supervisor for semiconductor manufacturing systems from scenario without choices in process flows to cases with choices which are common in modern manufacturing systems. To allow choices in process flows improves operational flexibility of these systems, it also requires more sophisticated supervisory control techniques. Built upon a directed graph model of process flows, the extended supervisor is able to efficiently avoid the deadlock state space explosion problem. Concepts such as compound events, operation strings and deadlock strings are restated. New concepts such as broken circuits, choice circuits, split events, merge events and so on are introduced. These concepts help to dramatically decrease the number of circuits that the supervisor has to check thus increasing efficiency of the method. Major features in the proposed method include: (i) it enables the optimal deadlock free operation of regular systems; and (ii) it runs in polynomial time (fast online computation) provided that the set of deadlock strings is calculated offline. Examples are provided to show the effectiveness of the method.