National Aerospace Laboratory (NAL) conducts the research program in which the unmanned supersonic research airplane will be developed to establish the design technology composed by Computational Fluid Dynamics (CFD). CFD analysis is necessary to develop next generation High Speed Commercial Transport (HSCT) which has high performances such as high lift-to-drag ratio. This paper describes the overview of a CFD code applied to the designing of the NAL's supersonic research airplane. It is also presented the recent problems for aerodynamic design with CFD.