Designing and implementing a Knowledge Management System (KMS) in a Virtual Enterprise is a labour intensive and risky task. Solution prototypes (Pilots) are usually built to verify system effectiveness prior to final implementation. The paper proposes a methodology to guide this Pilot specifications definition process. These guidelines support engineers and knowledge experts in collaboratively defining functionalities, services, software components and performance indicators of the prototype. The methodology has been conceived and applied within the European project VIVACE, to support the development of a Knowledge Enabled Engineering (KEE) system in the aeronautical domain.