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As equipment cost continues to grow in the capital investment of a fab, tool performance optimization has been critical to fab productivity and competitiveness. This paper addresses the optimization of tool operation sequence for efficiency, in specific, the design of a standard modeling process. The process consists of (1) Petri net (PN)-based modular modeling, which exploits an easily accessible freeware, (2) automatic synthesis of modules into a complete tool model and for simulation validation, and (3) conversion of the PN model to a mathematical formulation for optimization. A case study of a PVD cluster tool and its operation sequence control demonstrates that the standard modeling process enables engineers to systematically and quickly construct both simulation and mathematical models for tool sequence optimization and performance evaluation.