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Automated manufacturing systems are quite complex and varied in nature. Therefore, a practical approach to design software for managing manufacturing systems is to build generic solutions to the greatest possible extent, and then to customize them to suit the needs of each firm. Flexible manufacturing cell (FMC) plays more important role when production market becoming more competitive and manufacturing environment is often subject to change. Modular method for developing control software of FMC thus is necessary. Petri Net, a graphical modeling tool, allows the construction of models amenable both for qualitative and quantitative analysis. Over the last two decades, there have been many applications of using Petri Net for the modeling of manufacturing systems. In this paper, a modular approach by combining the PLC in equipment level and Petri Net in cell level for the development of FMC controller in a hierarchical manufacturing environment is addressed. Benefits of PLC and Petri Net thus can be fully utilized to develop an FMC controller. This generic FMC controller has been successfully implemented in several automated factories in Taiwan.