Aeroelastic codes based on Blade Element Momentum theory are the standard used by many wind turbine designers. These codes usually include models and corrections for unsteady aerodynamics, tip and root effect, tower shadow and other effects. In general, this kind of codes does not include models to correctly simulate aerodynamic control devices. This paper presents some modifications including the unsteady contributions due to the flap motion (based on indicial models) and the spanwise (3D) effects (based on circulation theory), in order to simulate flaps in the blades. This method can be included in BEM codes in general and it could also be applied to another kind of control devices. The validation and verification show the accuracy of this method using experimental data for two-dimensional unsteady cases, and CFD for three-dimensional steady and unsteady cases.