In complex systems' design, there is a need for an automated generalized methodology to evaluate and optimize a design with respect to a variety of System Design Factors (SDFs). In this paper, we present a methodology which allows the designer to specify their own hierarchical set of SDFs and the preferred models to evaluate those SDFs. This methodology can be used throughout many of the phases of the systems engineering life cycle. The use of the methodology will increase productivity in system design and reduce cost and improve effectiveness of the systems designed.