As the product lifecycle is getting shorter and various models should be released to respond to the needs of customers and markets, automation-based flexible production line has been recognized as the core competitiveness. According to these trends, system vendors supply cell-level systems such as FMC(Flexible Manufacturing Cell) that is integration of core functions of FMS(Flexible Manufacturing System) and RMC(Reconfigurable Manufacturing Cell) that can easily extend components of FMC. In the cell-based environment, flexible management for shop floor composed of existing job shop, FMCs and RMCs from various system vendors has emerged as an important issue. However, there could be some problems on integrated operation between heterogeneous cells to use vendor-specific cell controllers and on seamless information flow with high level systems such as ERP(Enterprise Resource Planning). In this context, this paper proposes process management systems supporting integrated shop operation of heterogeneous multi-cell based flexible manufacturing environment: First of all, (1) Integrated Shop Operation System to apply the process management system is introduced, and (2) Multi-Layer BOP(Bill-Of-Process) model, a backbone of the process management system, is derived with its data structure. Finally, application of the proposed model is illustrated through system implementation results.