An automated, simulation-based aircraft design process allows for the prediction of unanticipated problems early inthe design stage, leading to reduced turn-around time and development cost. Having reliable, and affordable (fast)design tools is crucial to achieving this level of automation in design process. An example of this is illustrated fora jet trainer aircraft using two aircraft design codes: Jet Designer and CEASIOM. A set of aerodynamic methodswith different degrees of fidelity and computational expense is considered, with the limitations of each methodprovided. In particular, this paper examines the challenges that CFD-based aircraft design poses to a designer,including: a) the cost of generation of large data tables, b) the automated handling of geometry, c) treating controlsurface deflections, d) and calculation of dynamic derivatives using CFD. A Kriging-based sampling approachwas used for generating aerodynamic tables with a reasonable computational cost compared with a brute-forceapproach. For Euler calculations, an automated CAD and mesh generation approach from a geometry descriptionwas used. It is demonstrated that application of Euler solutions to low fidelity aircraft geometry shows the expecteddesign trends. Also, results show that the wave drag at transonic speeds can be predicted with Euler equations, butnot with vortex lattice or Digital DATCOM. The treatment of control surface deflections was also investigated forthe vortex lattice solver and the Euler code. Transpiration boundary condition approach was used in the Euler codeto model the flap surface movements, although this approach is limited to small control surface deflections. Thecalculated aero tables form each aero source were used next to study the vehicle flying qualities. Results presenteddemonstrate the validity and feasibility of the simulation-based approach for aircraft conceptual design.