One of the advantages of atomic force microscopy (AFM) is that it can accurately measure the heights of targets on flat substrates. It is difficult, however, to determine the shape of nanoparticles on rough surfaces. We therefore propose a curvature-reconstruction method that estimates the sizes of particles by fitting sphere curvatures acquired from raw AFM data. We evaluated this fitting estimation using 15-, 30-, and 50-nm gold nanoparticles on mica and confirmed that particle sizes could be estimated within 5% from 20% of their curvature measured using a carbon nanotube (CNT) tip. We also estimated the sizes of nanoparticles on the rough surface of dried cells and found we also can estimate the size of those particles within 5%, which is difficult when we only used the height information. The results indicate the size of nanoparticles even on rough surfaces can be measured by using our method and a CNT tip.