This paper focuses on the vibration suppression task using an appropriate controller design for active control of structures with distributed piezoelectric actuators and sensors. The problem arises from the need to control undesired vibrations caused by disturbances or excitations acting upon a structure in an efficient and at the same time a simple way. A special class of disturbances/excitations ( periodical, with frequencies equal or near to the eigen-frequencies of the controlled structure) may cause undesired resonant states. In order to reject such disturbances and suppress vibrations in the presence of excitations an optimal LQ controller based on tracking systems with additional dynamics is proposed for the vibration control problem. The controller was tested in the presence of excitations with different frequencies. Controller design is model-based, where for the numeric modelling of the structure the finite element approach was used. Besides, subspace-based model identification was used as well. Controller design, testing and implementation were performed on the funnel-shaped shell structure, the inlet part of the magnetic resonance tomograph. Simulation results as well as the real-time implementation of the controller as a part of the Hardware-in-the-Loop system show considerable vibration suppression in the presence of excitations and confirm the efficiency of the controller.