This study presents the application of control methods in seismic mitigation of structural responses. The study consists of two parts. In the first section, fractional order filters are utilized to enhance the performance of the conventional LQR method for optimal robust control of a simple civil structure. The introduced filters modify the state variables fed back to the constant gain controller. Four combinations of fractional order filter and LQR are considered and optimized based on a new performance criterion defined in the paper. Introducing fractional order filters is shown to improve the results considerably for both the artificially generated ground motions and previously recorded earthquake data. In the second part, frequency dependent filters are introduced to improve the effectiveness of active control systems designed to mitigate the seismic response of large scale civil structures. These filters are introduced as band pass pre-filters to the optimally designed H2/LQG controller to reduce the maximum singular value response of input-output transfer matrices over a defined frequency range. Furthermore, a structured uncertainty model is proposed to evaluate robustness of stability and performance considering nonlinear force-deformation behavior of structures. The proposed perturbation model characterizes variations in the stiffness matrix more accurately, thereby reducing overconservatism in the estimated destabilizing perturbations. The aforementioned techniques are applied to the nonlinear SAC three story steel building. Numerical results indicate that introducing filters can enhance the performance of the system in almost all response measures, while preserving robustness of stability and performance.