This paper presents a comparison of two popular model reduction techniques on an aircraft model. Large scale model of the aircraft is obtained via Ground Vibration Test(GVT). In vibration based applications, natural frequencies are important, designers aims to focus on especially these frequencies. Therefore reduced order model should be obtained adequately by approximating original system at interested frequencies. In order to perform this, two popular model reduction methods; Frequency Weighted Balanced Model Reduction (FWBMR) and Rational Krylov based model reduction methods are resorted in this paper. Effectiveness of these two methods are discussed, and specifically flexibility of Rational Krylov based method is demonstrated on body freedom flutter aircraft model.