Trailing Edge Flaps on wind turbine blades have been studied in order to achieve fatigue load reduction on the turbine components. We show in this paper how Model Predictive Control can be used to do frequency weighted control of the trailing edge flaps in order to reduce fatigue damage on the blade root. The design model is based on a modal model of the blade structure and a steady state aerodynamic model of the blade airfoils. Depending on the output filter, loads within different frequency range are decreased. A fine tuning of the Kalman filter and of the cost function allows to decrease significantly the blade root loads without damaging excessively the trailing edge flap actuators.