Internal nonlinearities within piezoelectric actuators of Atomic Force Microscopes (AFM) still pose a great challenge for practicers in the area of nanotechnology. Especially, when topography of a large scale area is required along with high resolution, traditional scanning protocol will deteriorate the distortion of images. In this paper, a novel block scan and stitching method is proposed to mitigate such phenomena. By dividing the whole area into blocks and integrating them subsequently, creep, hysteresis and thermal drift within images can be reduced largely. Moreover, the whole procedure is executed in an automatic manner without human's intervention. Its feasibility is also verified by real experimental results.