Abstract: This study presents a new approach to model and analyse flexible manufacturing systems. This work takes place in a widest project of an automatic generator of control software. Our approach is divided into four steps: the first one deals with the physical description of the manufacturing system that is described by a specific notation. The second step builds the conceptual model with series of entities linked together. The following step models each link using controllable outputs Petri nets. A sequence of these Petri nets is obtained and the last step described their integration. An analyser-supervisor controls this integration operation. The results and interpretations given by the analyser provide information on the state of the system, more specifically on identification of potential deadlocks.