Purpose This study has compared morphological characteristics of dentin and enamel surfaces after cavity preparation by conventional methods and Er:YAG laser irradiation in different settings by using an Er:YAG laser scanner. Methods Thirty-five human teeth were randomly divided into seven groups that received cavity preparations as follows: G1 and G2 with high-speed drill with diamond and carbide burs, respectively, and G3 to G7 with Er:YAG laser scanner (λ = 2940 nm) operating at pulse energies (energy densities) of 420 mJ (840 J/cm 2 ), 490 mJ (980 J/cm 2 ), 560 mJ (1120 J/ cm 2 ), 630 mJ (1260 J/cm2) and 700 mJ (1400 J/cm2), respectively. The lased groups were treated with Er:YAG laser scanner in non-contact mode, keeping both frequency (20 Hz) and pulse duration (300 μs) fixed. Samples were sectioned and scanning electron micrographs of the lateral wall of the cavities were taken at different magnifications. Results The results showed that both groups of conventional cavity preparations exhibited enamel and dentin surfaces covered by smear layer, with no dentin-enamel boundary being identifiable. All lased groups showed clear enamel-dentin boundaries and clean surfaces of enamel and dentin with different micro-morphologies. The morphology of lased dental surfaces presented homogeneous alterations. Conclusions The Er:YAG scanner-assisted cavity preparation produced topographies in the entire dental surfaces and whose morphological characteristics were more favourable to further adhesion of resin restorations than the conventional ones.