In order to be competitive, every manufacturing organization has to adapt to changes occurring in its environment. This adaptability to changes is measured by the notion of "manufacturing flexibility" which is the ability that empowers a manufacturing organization to deal with internal and external uncertainties. Among organizational internal uncertainties, one major concern is how to deal with the practical situations of resource breakdowns. The objective of this study is to model, analyze and maximize performance of a multi- product, multi-stage and multi-line flexible manufacturing system in which all resources are studied under planned and unplanned breakdown conditions along with automated inspection required to ensure the quality of products at each manufacturing stage. This study uses colored Petri net method for FMS modeling because it can handle complex system modeling concepts and constraints in a compact way. The CPN models are simulated to generate resulting data which can subsequently be used for design of experiment modeling aimed to maximize the performance of a system.