In this dissertation, we introduce the fundamental ideas and constructs of Petri net models such as ordinary, timed, colored, stochastic, control, and neural, and present some studies that emphasize Petri nets theories and applications as extended research fields that provide suitable platforms in modeling, controlling, validating, and evaluating concurrent systems, information systems, and a versatile dynamic system and manufacturing systems;We then suggest some of extensions that help make Petri nets useful for modeling and analyzing discrete event systems and manufacturing systems models based on the context of a versatile manufacturing system, and applies extended Petri nets models to several manufacturing systems such as an assembly cell, an Automated Palletized Conveyor System, and a tooling machine to show increased modeling power and efficient analysis methods;Finally, Validation methods are presented for these models and results of a performance analysis from a deterministic and stochastic model are used to reorganize and re-evaluate a manufacturing system in order to increase its flexibility.