In this paper, a frequency-domain modeling methodology that can be applied to various multi-rotor aerial vehicles is introduced. The primary contribution of this work is a systematic integration of the first-principles modeling and system identification approaches to generate flight dynamics models with good accuracy. The first-principles modeling and model linearization are conducted to obtain an appropriate baseline model for the subsequent system identification. Next, a four-step parameter identification process, which consists of: (1) baseline model determination; (2) data collection and preprocessing; (3) mode-wise parameter identification; and (4) model fidelity validation, is performed in the frequency domain to identify the uncertain parameters. Our method has been applied to two custom-built multi-rotor aircraft (one X-type quadcopter and one QU4D quadcopter) for efficiency demonstration.