Enamel dissolution occurs when it contacts with acids produced by plaque bacteria, foods or drinks. There have been numerous and varied studies quantifying and characterizing the rate, extent and chemical aspects of enamel erosion; however, there is still hot debate about the amounts of enamel softening and loss. The objective of this study was to measure the enamel erosion process with high accuracy. Native third molars were partly eroded in citric acid (pH = 3.8) with some domains protected by a Ti coating layer. The surface morphology and structures before and after exposure to citric acid for different time periods were studied by AFM, SEM and nanoindentation, respectively. Based on this, the functions between the amounts of enamel softening, loss and erosion time were established for the first time. It was demonstrated that AFM, SEM and nanoindentation were suitable for measuring the early stages of enamel demineralization qualitatively and quantitatively.