The increasing use of fiber composite materials in the design of aircraft structures and the advent of easily available fast personal computers, have forced the aircraft design engineers to adopt complex mathematical models, which usually adress the trio of flight mechanics, aereoalsticity and controls in one simulation. The adoption of such kind of mathematical models also open a door for a robust methodology on the multidisciplinary optimization (MDO) of flexible/aeroelastic aircraft. This paper gives an overview of the a "closed-loop" design framework, which optimizes the structure of any given component like fuselage of the aircraft under dynamic loads. The objective is to reduce the weight of the given structure vis-à-vis maintaining the constraints of structural strength and the dynamic stability of the whole aircraft. An optimization problem is presented in the end, where the fuselage structure of a small executive jet is optimized under strcutural loads due to atmospehric turbulance.