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Modern manufacturing companies need flexible manufacturing control systems (FMCSs) to compete in today's unpredictable and ever-changing global markets. Traditional methodologies, however, can't meet the requirements of FMCS design. The function block (FB) concept in IEC61499 may provide a promising approach. In this present work, a FB based design pattern has been introduced to systematize the task of FMCS design in the IEC61499 context, which is enhanced by adopting formal reference models in the design cycle. The FB based framework and engineering methodology have been proposed, together with requirements specification of CASE tools to facilitate the development process. An illustrative example using the proposed design pattern is presented. When properly applied, it can substantially reduce the time and cost of systems engineering, while enhancing the flexibility, modularity, extensibility, reusability and interoperability of FMCSs.