This paper presents an approach for designing a robust vibration control system for a piezoelectric tube scanner (PTS) used in an atomic force microscope (AFM). In this control design, an uncertainty system model is constructed by measuring modeling error between the measured and model frequency response data. Then a minimax linear quadratic Gaussian (LQG) control technique is used to design a controller which minimizes scanner vibration at its resonant mode. This controller is robust against uncertainties introduced as a result of truncating higher order modes of the scanner, variation of plant transfer function due to temperature and humidity and measurement noise from the position sensors. The experimental results show that the proposed controller is able to reduce the vibration at its resonant mode and track the reference signal.