During the early phase of an aircraft program, Industrial Architects are evaluating different industrial scenarios. One of the activity is to perform trade-off to optimize the future industrial architecture using different performance parameters like Labor cost, Industrial assets cost, Lead Time and different kind of defect risks within the extended enterprise. For solving part of the problems, Product Line and Co-design concepts needs to be tackled. An Ontology-enabled MBSE approach and collaborative design process between the Aircraft and Industrial system domains will allow to overcome bottlenecks concerning knowledge management, interoperability and decision making in the design process.