Flexible Manufacturing Systems (FMSs) consist of machine tools capable of executing a wide range of machining operations relying on the fixtures to reference and block the parts. Hence, the constraints for their flexibility are shifted from the machines to the pallets. An interesting trend in the fixture market are zero-point fixture systems grounding on a clamping system that can hold standard baseplates where the fixture has been previously mounted. This allows a rapid and safe exchange of the baseplates without the need of realignment between the modular fixture and the pallet. In this paper we present an approach for rapid pallet configuration that exploits the additional level of flexibility provided by zero-point fixture systems. Grounding on an ontology-based data model, the description of the production process as a Network Part Program is used to evaluate the impact of rapid pallet configuration at system level and also how these degrees of freedom can be used in the management of the system. The steps of the approach are tested against a real industrial case provided by a company owning an FMS. © 2016 The Authors.