During the analysis and design of manufacturing systems, companies are challenged by existing restrictions and the running production. To deal with these key issues, different virtual factory approaches and tools have been widely implemented in recent years. By employing modern approaches and tools, a manufacturing system can be adapted effectively. Virtual reality (VR), one of the most important approaches, has recently been applied to the scientific and the industrial fields. Recent studies of VR applications are mainly focusing on the design of products, but not manufacturing systems. This paper presents VR as an innovative and collaborative design platform for manufacturing systems, which enables a holistic use of virtual factory tools. Based on this platform, three applications were implemented, which are addressed at different levels of a manufacturing system. Furthermore, a noise simulation and a virtual machining tool were visualised in a cave automatic virtual environment (CAVE).