Changes to the features of the enamel surface submitted to induced demineralisation and subsequent remineralisation were studied. The in vitro examination was conducted on polished slices of human molar teeth, divided in four groups: the untreated control (n = 20), challenged by a demineralisation with orthophosphoric acid (H3PO4) (n = 20), and challenged by a demineralisation following remineralisation with fluoride (F) varnish containing casein phosphopeptides (CPP) and amorphous calcium phosphate (ACP) compounds (n = 20). The specimens’ enamel surfaces were subjected to analysis of structure, molecular arrangement, mechanical features, chemical composition, and crystalline organization of apatite crystals. Specimens treated with acid showed a significant decrease in crystallinity, calcium, and phosphorus levels as well as mechanical parameters, with an increase in enamel surface roughness and degree of carbonates when compared to the control group. Treatment with fluoride CPP–ACP varnish provided great improvements in enamel arrangement, as the destroyed hydroxyapatite structure was largely rebuilt and the resulting enamel surface was characterised by greater regularity, higher molecular and structural organisation, and a smoother surface compared to the demineralised one. In conclusion, this in vitro study showed that fluoride CPP–ACP varnish, by improving enamel hardness and initiating the deposition of a new crystal layer, can be an effective remineralising agent for the treatment of damaged enamel.