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Force aroused from the contact of atomic force microscope (AFM) tip to a sample surface can induce compression of the sample due to its elasticity, thus causing the scanned height image of AFM to be lower than expected. A theoretical investigation of surface elasticity measurement and error compensation method is proposed in this paper. The error source of the height image is systematically demonstrated by analyzing the force curve of different materials in contact mode. Furthermore, an automatic surface elasticity measurement and error compensation method based on information fusion and parameter identification are proposed. In addition, Kalman filter is utilized to filter the compensated height image in order to eliminate system noise. Experimental results show the validity of the proposed compensation method and Kalman filter.