Modern technological industries fused with the Internet-of-Things (IoT) have been advancing rapidly. The joint usage of several technologies has led to the reshaping of the modeling and simulation techniques into the virtualization of physical systems. Thus, the concept of virtual prototyping has emerged as a significant development in distributed IoT applications that includes early exploration, optimization, and security assessments. Several industries have been employing various types of prototyping e.g., virtual platforms, digital twins, and application-specific virtualization techniques, to achieve individual development needs. In this chapter, we clarify some of these concepts and the distinctions between them, provide a comprehensive overview of various prototyping technologies, including digital twins, and discuss how several enabling technologies play a transformative role in the design and operation of intelligent cyber-physical systems.