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As the cost and complexity of constructing a semiconductor fabrication facility increases, responsive tools are needed for designing and planning its operations. Discrete-event simulation paired with design of experiments is an effective combination. This article demonstrates how simulation in combination with design of experiments is used to compare the intrabay layout of two automated material handling systems. The difference in stocker robot utilization, number of vehicle moves per hour, and average delivery time for the two intrabay layouts will be compared using a fractional factorial experimental design. The study demonstrates that the distributed storage option is preferable for maximizing manufacturing performance. Although the scope of this effort was restricted to a single situation, the solution procedure has general applicability as a tutorial for practitioners.