Modern flexible manufacturing facilities can be highly complex, consisting of the latest developments in machine tool technology, automated material handling systems and sophisticated cell controllers. The design and management of such systems requires a large number of decisions and choices with regard to production mix, assignment of fixtures and cutting tools. A large number of commercial computer modelling packages are now available in the market place. Although these allow valuable assistance in the analysis of a manufacturing facility, they usually take significant amounts of time to build models and require a large amount of training, and can be constraining in their application. This paper establishes a research prototype for a multi-level approach for the realization of a three-phase design and modelling system for flexible machining facilities. It portrays the view of an integrated fully data-driven solution underpinned by a machining cell database, and outlines three major areas of work within the structure, i.e. the 'Cell Configurator', 'Evaluator' and 'Emulator'. The approach is demonstrated and supported throughout the paper by an industrial case study of a modern three-machine flexible machining cell, illustrating the use of the underlying methodology behind the approach and typical inputs/outputs at each phase. The final part of the paper provides a discussion of the approach adopted based on user comments and in relation to commercial simulation tools available.