To face an increasingly competitive environment within a globalization context, and to focus on core high-added value business activities, enterprises have to establish partnerships with other companies specialized in complementary domains. Such an approach, primarily based on optimization of the value chain, is called virtualization of the Enterprise. Enterprises relying on virtualization, sub-contracting and outsourcing have to coordinate activities of all the partners, to integrate the results of their activities, to manage federated information coming from the different implied information systems and to re-package them as a product for the clients. The adopted organization, which is considering as well as the internal and external resources, is called “Extended Enterprise”. Nevertheless, in such complex emerging networked organizations, it is more and more challenging to be able to interchange, to share and to manage internal and external resources such as digital information, digital services and computer-enacted processes. In addition, digital artifacts produced by enterprise activities are more and more heterogeneous and complex. After characterizing expected interoperability for collaborative platform systems and highlighting interoperability issues and brakes not yet addressed, this chapter describes an innovative approach to build interoperability based on a Federated Framework of legacy eBusiness standards of a given ecosystem. It implies facing important issues related to semantic preservation along the lifecycle of the artifacts and infrastructures required to define and exploit an application. We present two use case studies that apply interoperability strategies.