A static control system architecture cannot meet the demand for continually introducing new parts into manufacturing systems while maintaining high quality and throughput for existing parts; a reconfigurable control infrastructure is needed. Control authority in the factory is typically allocated to three levels: the machine, cell, and system. The machine controllers must be reconfigurable to process different parts, the cell controllers must be reconfigurable to adapt to different part flows, and the system level controller must be reconfigurable to adapt to new parts in the system. In this paper, we describe the reconfigurable control infrastructure that we have developed at the University of Michigan's reconfigurable factory testbed. We then show through example how this infrastructure enables the real-time reconfiguration of the controllers at the machine and cell levels to adapt to quality problems and unexpected faults