This paper describes the design of a tool for rapid analysis and implementation of flexible material handling systems. The work incorporates a commercial discrete-event and 3D animation simulation system and extends its functionality with respect to material handling systems. Logical clusters of commercial, modular conveyor components are defined and installed as additions to the simulator's component libraries. These logical groupings, plus the material-flow logic specified by the user in a given simulation analysis, are used to enable automatic generation of control code for the corresponding physical implementation of the simulated system. Key elements in accomplishing this connection are the definition of component logical groupings and a novel, reactive-agent based software organization of the real-time material-handling control code.