A general form of boundary element method for incompressible flow has been developed using Green's function. An integral equation of the perturbation velocity potential is obtained. On the paneldivided surfaces, this results in a set of linear algebraic equations. The pressure distribution on complete aircrafts including wing, body, and tail can be found using present method. Two examples of fuselage design problem for low drag are presented, in which the frictional drag is approximated with the local velocity and the surface area. Flexible modification of fuselage shape is obtained by using spline surfaces. One of the examples shows a practical application of the method for flow separation prediction.