Atomic Force Microscope (AFM) is a very strong and beneficial instrument for acquiring images at nanometer scale. Hence, obtaining better image quality and scan speed is a research area of great interest. Improving the dynamic responses of the scanning probe and the vertical motion of the scanner mechanisms are the two major areas of concentration in this sense. Improving the vertical dynamics is achieved either by designing more complex scanner mechanisms with higher bandwidth or designing more sophisticated controllers rather than the PI, PID or PhD types of controllers that are mostly used in practice. In this paper, the authors focus on designing a repetitive control scheme for fast and accurate scanning. It is possible to implement repetitive control to achieve this goal when it is considered that the successive lines of the scan are quite similar due to the very small steps taken to advance on the sample. Repetitive control can reject higher frequency disturbances due to the surface topography in AFM much better than a conventional controller can, as it can drive the error caused by any periodic input signal to zero. Besides increasing the scan speed, it is also important that the phase lag can be compensated perfectly using repetitive control, with the knowledge of the surface topography from the previous period by introducing appropriate phase advance.