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This study aims to optimize a pull type multi-product, multi-line and multi-stage Flexible Manufacturing System whose resources are subject to breakdown conditions. To ensure continual supply of the finished products, under breakdown conditions, the parts/ materials are flowing through alternate routes exhibiting routing flexibility. Every machining and assembly station has been equipped with automated inspection units to inspect the quality of the products. The system is modeled through Colored Petri net methodology and the impact of input factors has been shown on the performance of the system. The study explores multi-factor optimization using Design of Experiment and Response surface Methods.