The Magellan Telescope Adaptive Optics System (MagAO) is subject to resonance effects induced by elements within the system instrumentation, such as fans and cooling pumps. Normalized PSDs are obtained through frequency-based analysis of closed-loop on-sky data, detecting and measuring vibration effects. Subsequently, a space-state model for the AO loop is obtained, using a standard AO loop scheme with an integrator-based controller and including the vibration effects as disturbances. Finally, a new control alternative is proposed, focusing on residual phase variance minimization through the design and simulation of an optimal LQG control approach.