The paper introduces a functional shape parametrization approach for the design and the optimization of unconventional aircraft configurations. The proposed design methodology is tailored for the preliminary design stages, and it is based on the use of mixed fidelity simulations. The approach is integrated in the DLR collaborative design framework, which makes use of a centralized model, and distributed analysis modules. The overall design process is applied for the multidisciplinary shape optimization of a Blended Wing Body configuration, including a large number of design variables. Single and multi-objectives optimization problems are formulated, and the optima designs are compared and discussed.