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Modern microelectronics manufacturing may be described by re-entrant manufacturing systems (ReMS). To be competitive, ReMS are designed to run fully automated and effective production control and schedule policies are pursued, however, a high-fidelity system model is the prerequisite. In this paper, an extended object-oriented Petri nets (EOPN) is proposed to cope with the complexity of re-entrant process routes and mixed production modes. To ensure the resulting EOPN model is deadlock free, an algorithm is introduced to analyze the resulting EOPN model so that all possible deadlock situations may be detected and avoided before any control and schedule policy is implemented. In addition, formal description of the related conflicts and resolving algorithm are also presented in this paper.