A prototype results from the need to verify various qualities of the product at different stages of its development. In set-based design, multiplying prototypes is particularly critical to enable a broad exploration of the design space before committing to a solution. The exploration targets the choice of the best of all viable concepts on one hand but on the other hand also focuses on documenting them to better orient the search during the next attempts. This ultimately contributes to gradually improving the company’s engineering knowledge. According to current aerospace industry practices and considering the set based development paradigm in Lean thinking, an approach to handle multiple prototypes information with Digital Mock-Up (DMU) technologies is forwarded in this paper. This approach postulates that prototyping and testing activities may be supported by a Manufacturing Process Management (MPM) solution with a special use of three key functionalities, namely: Product Data Management (PDM) and MPM instantiation, MPM links, and Configuration Management (CM). These aspects are essential when handling multiple prototyping sets along with their test results.