In a real manufacturing system, faults are events that occur and should be considered as a relevant fact. However, most research considers only description and optimization of normal processes. In this book, a methodology for modeling, analyzing, and integrating fault detection and treatment with the normal processes is introduced. The objective is to prove that an approach for modeling and analyzing manufacturing systems considering all processes is essential for improving flexibility and autonomy. These systems can be analyzed from a point of view of discrete event dynamic systems (DEDS). From the DEDS context, a methodology based on Petri nets is introduced, which considers fault detection and treatment in a modular and hierarchical structure. The modular characteristic permits the association of tree types of processes: normal, fault detection, and fault treatment processes; and the hierarchical characteristic permits the integration by hierarchical levels based on top-down and bottom-up approaches. Case studies are considered, in which, analytical and simulation tests are conducted to validate the proposed methodology.