In early design stages of aircraft, component sizing is to a large extent based on semi empirical methods, which are generally lacking for unconventional aircraft configurations. This increases the uncertainty of the performances of the generated design, such as its stability and controllability. This work aims at using a more physics-based approach for predicting stability and control derivatives estimation during early design stages. A 3D panel method is chosen, which predicts the stability and control derivatives 32% more accurate than a vortex lattice solver. An acceptable run time is achieved by creating a new version of an in-house Knowledge Based Engineering tool, which reduced pre-processing time by 96% compared to manual use of the analysis tool. This methodology is then used to predict the stability and control derivatives of two box wing aircraft, and one conventional aircraft, which have been designed for similar requirements.