As current high-speed scanning Atomic Force Microscope (AFM) is mainly designed for the biological imaging application and its scanning speed and scanning range should be improved, a novel high speed AFM was designed. Based on the flexure guide structure driven by piezo actuators, the AFM scanner with a large range was proposed, by which the AFM scanning range is expanded to 100 μm×100 μm in the x-y directions. By the Fourier expansion, the high harmonic characteristics of the common triangle and sinusoidal driving signals were analyzed, and their effects on the high speed scanning image were discussed. To avoid the mechanical self-oscillation of the stage during scanning, the sinusoidal driving signal was taken to drive the high speed scanning and the line-scan speed was up to 50 line/s. Finally, a new method to eliminate AFM nonlinearity error based on positioning sampling was designed. This method effectively reduces the image distortion resulted from nonlinear errors of the AFM scanner.