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In order to reduce manufacturing control software design cycle and costs, it is imperative to reuse off-the-shelf software components, ensure system properties at design time, and automate software design process. To this end, a component and an agent-based plant modeling of three structures and systematic controller synthesis approaches are proposed under a hierarchical flexible manufacturing system (FMS) architecture. That is, the static structure is modeled using class diagrams of Unified Modeling Language (UML); the dynamic structure is modeled using Petri net (PN); the functional logic is modeled using rule sets. A plant PN controller can be derived systematically with the approach proposed in this article while the desirable system behaviors (e.g., liveness and cyclicness) will be obtained.