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Our objective is to develop a general and versatile approach for building structured formal models of complex automated systems in order to facilitate their control and diagnosis. For this purpose, we present a methodology that builds the complete model of a system by composing models of the individual hardware components, their physical coupling, and the associated control logic. We choose to employ a hierarchical decomposition that separates the control logic into a high level that manages the sequence of control actions and a low level that implements the control actions. The low level is composed of control logic and physical components (sensors and actuators) grouped into a device. In order to capture the physical constraints between the components in a device, we propose the notion of a physical constraint automaton, which is composed with the generic component automata to generate the complete model of the device. We also show how the methodology allows the introduction of component faults into the overall model. The effectiveness of the proposed approach is demonstrated on a micro flexible manufacturing system.