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This paper reports the application of software engineering techniques to the analysis and design of logic and supervision control software for a complex manufacturing system, with particular regard to PLC-based control architectures. The design methodology presented in the paper relies on a mechatronic approach to the modularization of the whole problem, so that an efficient system decomposition can be performed, in order to reduce complexity of the software development task and increase flexibility and maintainability of the application. Modeling concepts derived from both object-oriented and structured analysis methods have been used to describe system modules and behaviour. However, some adaptations have been introduced, because the peculiarities of the manufacturing systems domain were difficult to express within an existing software design method. A practical case of study for the application of the design methodology proposed show that software engineering techniques can be applied successfully even in the unusual field of PLC-based control of manufacturing systems.