Cyber-physical systems (CPS) integrate both physical and computational elements and their engineering requires bridging the continuous analog real world and the discrete digital world. User interfaces of cyber-physical systems belong to the class of command and control systems and their design and engineering usually follow ad-hoc craft processes highly parametrized by the very nature of the physical component(s). This paper proposes a systematic approach for engineering CPS, emphasizing the problems and possible solutions to design and assess their user interfaces (both control and presentation). The paper first proposes a generic architecture for CPS going from the physical element(s) to the user interface. This architecture is then refined, highlighting the behavior and software interfaces of each of its component and showing how information and control from the physical elements have to be processed and transformed to make sense to the operator. The paper presents extracts of the application of the proposed approach to the command and control cockpit application of an aircraft system.