AFM is used to study tooth surfaces (enamel and cementum) in order to compare the pattern of particle distribution and demineralization process in the two dissimilar tooth hard tissues. Our approach is focusing mainly on the qualitative observations of tooth surface morphology and quantitatively measuring the early stages of mineral loss. The native enamel presented globular particles tightly packed. After polishing the aprismatic layer, the particles observed were relatively larger and more organized than ones in the outmost enamel surface. The cementum had small grains arranged in some degree of ordered packing with varying crystallite orientations. After different time treatment with citric acid solution, all the sample surfaces became more irregular and had the deeper grooves. The maximum mineral loss was greatest for the cementum sample and lowest for the native enamel. The demineralization difference between the enamel and cementum shows the structure and component play important roles in the morphological changes of demineralization. These demonstrate that the microstructure and demineralized difference between enamel and cementum obtained with AFM are complementary to the usual SEM images and TEM data. AFM is suitable for measuring early stages of tooth surface demineralization.