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For some wafer fabrication processes, such as an atomic layer deposition (ALD) process, the wafers need to visit some process modules for a number of times. Using the existing swap-based strategy scheduling method in such systems leads to a 3-wafer cyclic schedule. Unfortunately, it is not optimal in the sense of cycle time. Aiming at searching for a better schedule, this paper models the system by a timed Petri net. With this model, the properties of the 3-wafer schedule are analyzed. Then, based on the analysis, it is found that, to improve the performance, it is necessary to reduce the number of wafers completed in a cycle. Hence, a 1-wafer schedule is developed by using a new swap-based strategy. By using the Petri net model, its cycle time is analyzed and shown to be optimal. Also, an effective method is presented to implement it. Illustrative examples are given to verify the research results obtained in this paper.