The use of modelling tools for the design of industrial systems is increasingly replacing the documentation production resulting from a classic system design process. One of the problems to be solved in order to fully succeed in this transition is information confidentiality management. It is also necessary to propose a system design process that allows an evolution through the whole design life cycle, and that guarantees a coherent design for a given level of confidentiality. To the best of our knowledge, neither current Model Based System Engineering (MBSE) tools, nor academic research propose solutions to this specific issue. In this paper, we propose a model based system design process to manage elements belonging to different levels of confidentiality. The process guarantees a plurality of confidentiality levels in line with Bell-Lapadula security policies for the secure management of system design and specification, as required for the protection of national and coalition defense information. It includes the separation into enclaves and adaptations guaranteeing the preservation of confidentiality and integrity to authorized users. We describe how this process can be leveraged for current modelling tools by exploiting existing multi-user functionality.