The paper illustrates the role of modeling of shop floor to support an innovative solution for the control architecture of automated manufacturing systems. One of the main characteristics of manufacturing systems domain is, in fact, the variety of configurations that manufacturing systems can assume and this may prevent the possibility to easily adapt and reconfigure the control solution for advanced manufacturing systems. To this end, the paper presents a proposal on how to cope with this issue, coming from a collaborative project, where important European universities and companies are involved. The proposal is based on a structured modeling (i.e. ontology) of manufacturing systems. The paper proposes a practical example of the modeling, envisioning how this can be then exploited within the proposed architecture that defines a new concept of the Manufacturing Execution System of manufacturing equipment.