Flexible hybrid assembly systems have been touted to be a feasible solution to the paradox of flexibility to produce a high mix of products, while maintaining the capabilities of mass production of dedicated equipment. While increasing flexibility does aid in handling the technology barriers, a robust design, planning and optimization infrastructure is needed to monitor, control and execute such a complex manufacturing environment. The planned system should comprise of process planning, simulation, validation and optimization tools, all working in synchrony and with a unified data structure available to all systems.