To cope with quick variation in product demand, modern automation systems shall be able to conjugate increasing complexity of controlled processes with agile reconfiguration of flexible manufacturing systems. To such an aim, structured approaches for reconfigurable system design, based on formal reference models, have to be provided. Mandatory condition for the adoption of such approaches is the identification of methodological guidelines, capable to proof their foundation and validity on real industrial application cases. In such a context, present paper describes main steps of a structured control system development approach -starting from UML based specification, integrating IEC 61499 based control design and closed-loop simulation based verification techniques -focusing a real industrial plant.