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Sonic boom annoyance is an important technical showstopper for commercial supersonic aircraft operations. It has been proposed that aircraft can be shaped to alleviate sonic boom. Choosing the right aircraft shape reflecting the design requirements is a fundamental and most important step that is usually over simplified in the conceptual stages of design by resorting to a qualitative selection of a baseline configuration based on historical designs and designers perspective. Final aircraft designs are attempted by minor shape modifications to this baseline configuration. This procedure may not yield large improvements in the objectives, especially when the baseline is chosen without a rigorous analysis procedure. Traditional analyses and implementations tend to have a complex algorithmic flow, tight coupling between tools used and computational limitations. Some of these shortcomings are overcome in this study and a diverse mix of tools is seamlessly integrated to provide a simple, yet powerful and automatic procedure for sonic boom minimization. A shape optimization procedure for supersonic aircraft design using better geometry generation and improved analysis tools has been successfully demonstrated. The geometry engine provides dynamic reconfiguration and efficient manipulation of various components to yield unstructured watertight geometries. The architecture supports an assimilation of different components and allows configuration changes to be made quickly and efficiently because changes are localized to each component. It also enables an automatic way to combine linear and non-linear analyses tools. It has been shown in this study that varying atmospheric conditions could have a huge impact on the sonic boom annoyance metrics and a quick way of obtaining probability estimates of relevant metrics was demonstrated. The well-accepted theoretical sonic boom minimization equations are generalized to a new form and the relevant equations are derived to yield increased flexibility in aircraft design process. Optimum aircraft shapes are obtained in the conceptual design stages weighing in various conflicting objectives. The unique shape optimization procedure in conjunction with parallel genetic algorithms improves the computational time of the analysis and allows quick exploration of the vast design space. The salient features of the final designs are explained. Future research recommendations are made.