The concept of combining the power of several independent factories to achieve complex manufacturing processes as so-called virtual manufacturing enterprises is not new and has been addressed by several research projects in recent years. However, there is still a need for adequate methodological support and tools for modelling, structuring and controlling of the next generation of manufacturing systems, such as the virtual factory. In this research, a conceptual virtual factory reference model is presented with the goal to provide companies with general guidelines to manage and monitor the business processes that are needed to create, execute, and dissolve a virtual factory. The virtual factory reference model was built taking into account industrial’s requirements and by reviewing the literature in several relevant fields of research such as collaborative networks, supply networks, manufacturing networks, supply chain management, and business processes. Afterwards, it has been validated through its application to future virtual factories of three different industrial sectors: machinery, energy, and semiconductor.