In this paper dynamic modeling parameters were estimated using a frequency domain estimation method. A systematic flight test method was employed using preprogrammed multistep excitation of the swashplate control input. In addition when one axis is excited, the autopilot is engaged in the other axis, thereby obtaining high-quality flight data. A dynamic model was derived for a small scale unmanned helicopter (CNUHELI-020, developed by Chungnam National University) equipped with a Bell-Hiller stabilizer bar. Six degree of freedom equations of motion were derived using the total forces and moments acting on the small scale helicopter. The dynamics of the main rotor is simplified by the first order tip-path plane, and the aerodynamic effects of fuselage, tail rotor, engine, and horizontal/vertical stabilizer were considered. Trim analysis and linearized model were used as a basic model for the parameter estimation. Doublet and multistep inputs are used to excite dynamic motions of the helicopter. The system and input matrices were estimated in the frequency domain using the equation error method in order to match the data of flight test with those of the dynamic modeling. The dynamic modeling and the flight test show similar time responses, which validates the consequence of analytic modeling and the procedures of parameter estimation.