In this paper a new manufacturing control architecture for flexible manufacturing systems is proposed, with the objective of improving their reconfigurability, adaptability, scalability and performance. To do so, this research focuses on two key aspects: improving the structure of the control model and integrating the process plans into the manufacturing control itself. The reconfigurability of the system is achieved through the utilization of a holarchic architecture made up of IEC61499 function blocks, which act as autonomous and distributable entities. Adaptability and performance are improved by integrating the feature-based process plans of the parts into the control tasks. These plans are modelled using the STEP-NC standard reference models to allow the effective integration of non-linear plans into the manufacturing control. As a result, resources utilization is improved and performance is increased, thereby allowing the size of the system design to be reduced.