In a flexible manufacturing system, a cell controller is able to identify and evaluate a number of alternative decisions to meet the objectives set by the factory level controller. In this paper, a Petri net-based cell controller is presented to accomplish this task. A static model is developed by using the Integrated Computer Aided Definition(IDEF0) method to represent clear functional relationships among the objects of the system. Based on the static model, two Petri net models are developed for the physical part flow and for the information flow. Multiple decision alternatives are generated from the physical part flow model and are synchronized with the information flow model for execution of the selected alternative.