Central to compressing engineering development times for complex cyber-physical systems is the identification of reasonable alternatives early in the design cycle. This paper describes the development and use of an ontology to quickly prune the conceptual design space for cyber-physical systems engineering. The Georgia Tech Aerospace Systems Design Laboratory, Metamorph Inc., and Raytheon refined an approach originally piloted on amphibious ground vehicles to determine whether it could be generalized to other product domains. Reducing the design space early in the engineering life cycle enables designers to focus quickly on high-value alternatives to reduce cost and speed development. The OpenMETA tool suite, supported by semantic constructs for model integration, facilitates trades and analysis across the engineering disciplines, including electrical, mechanical, thermal, fluid, and cyber. The ontology developed by the authors and described in this paper provides the semantic underpinnings to encode relationships among design alternatives and quickly visualize these trades.