This study evaluated the structural changes of enamel treated by the Regenerate system and carbon dioxide (CO2) laser against acid challenge. Thirty human enamel slabs were prepared and assigned into three groups: Group I: untreated (control); Group II: treated with the Regenerate system; and Group III exposed to CO2 laser. All specimens were subjected to an acid challenge (pH 4.5–7.0) for 14 days. Specimens were evaluated and compared at 120 points using five Raman microspectroscopic peaks; the phosphate vibrations ν1, ν2, ν3, and ν4 at 960, 433, 1029, and 579 cm−1, respectively, and the carbonate at 1070 cm−1, followed by Vickers microhardness test. The ratio of carbonate to phosphate was correlated to the equivalent microhardness numbers. The intensities of phosphate peaks ν1, ν2, and ν4 were reduced in all groups post-acid challenge, while the carbonate and ν3 were significantly increased (p < 0.000). Surfaces treated by Regenerate exhibited higher peak intensity of phosphate and carbonate before and after pH-cycling (p < 0.05). The mineral content in enamel had a direct effect on tissue microhardness, and the CO2-lased surfaces showed a reduced carbonate content and higher microhardness values. Both approaches induced surface changes that can protect enamel against acid challenge resulting in a significant benefit for dental healthcare.