This research delves into semantic interoperability for 3D virtual commissioning (VC) applications, varying from single-level to multi-level interoperability. For single-level interoperability, the interoperability between 3D emulation and between discrete event simulation (DES) software applications is considered. Currently, a comprehensive data format is still in demand to achieve full-scope interoperability between 3D VC software applications. In this case, a case-driven iterative approach is developed to extend a data format towards a comprehensive generic VC data model. For single-level interoperability, AutomationML is selected as the initial data format for interoperability between 3D emulation software applications, while Core Manufacturing Simulation Data (CMSD) is chosen for interoperability between DES software applications. The two standards are subsequently extended based on the proposed case-driven iterative approach. As a result, 97.5% attribute conversion rate between 3D emulation software applications is achieved via AutomationML extension, while 80.2% attribute conversion rate between DES software applications is achieved via CMSD extension. Regarding multi-level interoperability, 31.0% of CMSD extension attributes can be converted from attributes in AutomationML extension, while the conversion rate is 13.1% the other way around. This creates an opportunity to reuse data and keep model consistency between 3D emulation and DES software applications.