This paper presents a methodology for the design of the primary flight control surfaces, in terms of size, number and location, for fixed wing aircraft (conventional or unconventional). As test case, the methodology is applied to a 300 passenger variant of the Prandtl Plane. This box wing aircraft is deemed to have low induced drag compared to conventional aircraft. The methodology is completely physics based and includes an aerodynamic analysis, followed by a control allocation algorithm and an analysis of the flight mechanics. The design has to fulfill a set of handling qualities requirements with a minimum total control surface area. An optimization algorithm is used to find the best design. Results indicate that this is possible with ailerons outboard on both wings, elevators inboard on both wings and conventional rudders in the vertical tail. The configuration allows for pure torque control and also direct lift control in the longitudinal axis. These features can potentially enhance airfield performance. Nomenclature