Helicopters are versatile vehicles that can vertically take off and land, hover, and perform maneuver at very low forward speeds. These characteristics make them unique for a number of civilian and military applications. However, the radial and azimuthal variation of dynamic pressure causes rotors to experience adverse phenomena such as transonic shocks and 3-D dynamic stall. Adverse interactions such as blade vortex interaction and rotor-airframe interaction may also occur. These phenomena contribute to noise and vibrations. Finally, in the event of an engine failure, rotorcraft tends to descend at high vertical velocities causing structural damage and loss of lives. A variety of techniques have been proposed for reducing the noise and vibrations. These techniques include on-board control (OBC) devices, individual blade control (IBC), and higher harmonic control (HHC). Addition of these devices adds to the weight, cost, and complexity of the rotor system, and reduces the reliability of operations. Simpler OBC concepts will greatly alleviate these drawbacks and enhance the operating envelope of vehicles. In this study, the use of Gurney flaps is explored as an OBC concept using a physics based approach. A three dimensional Navier-Stokes solver developed by the present investigator is coupled to an existing free wake model of the wake structure. The method is further enhanced for modeling of Blade-Vortex-Interactions (BVI). Loose coupling with an existing comprehensive structural dynamics analysis solver (DYMORE) is implemented for the purpose of rotor trim and modeling of aeroelastic effects. Results are presented for Gurney flaps as an OBC concept for improvements in autorotation, rotor vibration reduction, and BVI characteristics. As a representative rotor, the HART-II model rotor is used. It is found that the Gurney flap increases propulsive force in the driving region while the drag force is increased in the driven region. It is concluded that the deployable Gurney flap may improve autorotation characteristics if deployed only over the driving region. Although the net effect of the increased propulsive and drag force results in a faster descent rate when the trim state is maintained for identical thrust, it is found that permanently deployed Gurney flaps with fixed control settings may be useful in flare operations before landing by increasing thrust and lowering the descent rate. The potential of deployable Gurney flap is demonstrated for rotor vibration reduction. The 4P harmonic of the vertical vibratory load is reduced by 80% or more, while maintaining the trim state. The 4P and 8P harmonic loads are successfully suppressed simultaneously using individually controlled multi-segmented flaps. Finally, simulations aimed at BVI avoidance using deployable Gurney flaps are also presented.