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This paper addresses the issue of modelling concurrent systems whose structure is subject to changes by using an extension of the Petri nets formalism. Within this scope, we introduce the concept of reconfigurable finite capacity Petri nets and we apply it to a flexible manufacturing system model. Besides providing the designer a facile means of expressing the dynamic character of the flexible manufacturing system, the formalism also simplifies the model. In the second part of the paper we present and also compare the Petri net model and the equivalent reconfigurable finite capacity Petri net model for a such a system and we evaluate these models using PetriNetExec, a software library supporting the integration of Petri nets into Java applications.