We suggest uncertainty compensation methods for the quantification of nanoscale indentation using atomic force microscopy (AFM). The main error factors in the force-distance curves originated from the difference between theoretical and real shape of AFM tip during nanoscale indentation measurements. For the uncertainty compensations of tip shapes and misalignment of loading axis, we applied the enhanced tip geometry function and Y-scanner moving to the AFM measurements. Three different materials such as Si wafer, glass, and Au film were characterized with these compensation methods. By applying compensation methods, our results show the decreased values from 167% to 39% below 100 nm indenting depth compared with the literature values. These compensation methods applied to thin films will show the advanced quantitative analysis of hardness measurements using nanoscale indenting AFM. (C) 2013 Elsevier B.V. All rights reserved.