The High Fidelity Multidisciplinary Optimization (HFMDO) 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) has been working to deliver a modular design environment suitable to high fidelity analysis and design of coupled systems. Some of this work has involved partnering with Phoenix Integration (developer of the industry standard ModelCenter framework) to combine the specialties of MDAO and framework design. The HFMDO System has been developed using multiple, incremental builds. This paper describes Build 3.1 and Build 4.0. Build 3.1 is a culmination of previous builds that has resulted in a complete high fidelity MDAO system featuring capabilities such as multi-fidelity aerodynamics and parametric finite element model generation. Build 3.1 implements the High Speed Civil Transport (HSCT) configuration and a trade study and optimization of this supersonic vehicle configuration is also presented. Build 4.0 addresses the need to balance a high fidelity MDAO system with robust system design. Build 4.0 implements the N+2 Supersonic Transport configuration and is the final build of the HFMDO System.