System architecture is defined as the description of a complex system in terms of its functional requirements, physical elements and their interrelationships. Designing a complex system architecture can be a difficult task involving multi-faceted trade-off decisions. The system architecture designs often have many project-specific goals involving mix of quantitative and qualitative criteria and a large design trade space. Several tools and methods have been developed to support the system architecture design process in the last few decades. However, many conventional problem solving techniques face difficulties in dealing with complex system design problems having many goals. In this research work, an interactive multi-criteria design optimization framework is proposed for solving many-objective system architecture design problems and generating a well distributed set of Pareto optimal solutions for these problems. System architecture design using multi-criteria optimization is demonstrated using a real-world application of an aero engine health management (EHM) system. A design process is presented for the optimal deployment of the EHM system functional operations over physical architecture subsystems. The EHM system architecture design problem is formulated as a multi-criteria optimization problem. The proposed methodology successfully generates a well distributed family of Pareto optimal architecture solutions for the EHM system, which provides valuable insights into the design trade-offs. Uncertainty analysis is implemented using an efficient polynomial chaos approach and robust architecture solutions are obtained for the EHM system architecture design. Performance assessment through evaluation of benchmark test metrics demonstrates the superior performance of the proposed methodology.