Recent trends in the flexible manufacturing systems are morphing cell control for the shop-wide production operation system and providing the integrated operation and execution system together with vendor-specific FMC/FMS platform. In these requirements, the shop-floor level operation system plays a role of coordinating the control activity of each cell, and has to provide flexibility for the complexity of mixed operations of various cells. This paper suggests a system architecture for the mixed environments of multi-cells and job shop, its corresponding enabling technologies based on comparative studies with other related studies and commercialized systems. This approach includes a process definition model considering the integration with upper BOM-BOP and external service modules, and reconfigurable device-level interface which provides dynamic interconnections with machine tools and cell controllers. The function modules and their implementation results are also described to provide the feasibility of the proposed approaches as the flexible shop-floor operation system for the multi-cell environments.