The High Fidelity Multidisciplinary Optimization application delivers physics-based multidisciplinary analysis and optimization (MDAO) capabilities that are required to develop next generation supersonic aircraft. The software tools and approaches accurately model prediction of vehicle performance, interdisciplinary couplings, and system-level evaluation of the benefits and risks. M4 Engineering (experts in high-fidelity MDAO processes) is working with Phoenix Integration (developer of the industry standard ModelCenter MDAO framework) to combine their specialties to deliver a modular design environment suitable to high fidelity analysis and design of coupled systems. The key elements of this toolset include an object-oriented integration framework, common objects and analysis modules based on custom data types. The HFMDO system utilizes Geometry Manipulation by Automatic Parameterization (GMAP) and RapidFEM for advanced parametric geometry and grid generation technology for aerodynamic and structural models. M4 Engineering and Phoenix Integration are developing the HFMDO System using multiple, incremental builds. This paper describes the capabilities of Build 2 of the HFMDO System, which includes modules for addressing the disciplines of Geometry, Aerodynamics, Propulsion, Structural, Stability & Control, and Mission. A trade study and optimization of a supersonic vehicle configuration is also presented.