Supersonic business jet design is a complex process to balance highly stringent environmental requirements in addition to the usual performance measures. Conceptual aircraft designs obtained by employing simplified analyses would be compromised in some respect when the concept is transferred to further stages of design. To overcome this problem, improved analysis methods for conceptual aircraft design are developed in this study. Geometry is parameterized using many shape parameters to create any arbitrarily complex aircraft shape. The aerodynamic flow field near the aircraft is obtained in an automated fashion using three dimensional panel methods. Sonic boom propagation is carried out considering atmospheric variations, thermo-viscous absorption, molecular relaxation and diffusion phenomena. The optimization results obtained elsewhere using simple linear methods are analyzed using the methods developed here and the responses are compared. Shortcomings of the traditional approaches are discussed and future work using these improved methods is suggested. Nomenclature c Ambient speed of sound.