We measured three-dimensional shape of a specimen of calcareous nannofossil by using an atomic force microscope (AFM), and traced its change during an aqueous dissolution experiment. Some numerical values are calculated to characterize the shape changes of the specimen upon dissolution; volume, surface area, and roughness of the specimen decreased by the dissolution. The present AFM method is expected to study quantitatively possible changes in calcareous nannofossil assemblage due to different dissolution rates for different fossil forms.