Aims: The aims of the present study were to examine the surface topographies of intact HyFlex CM and HyFlex EDM nickel-titanium files and to compare alterations in the surface topographies of these files after root canal preparation of severely curved canals of molar teeth. Methods: Eight HyFlex CM (25/.08) and 8 HyFlex EDM (25/.08) files were included in the present study. In total, 64 severely curved canals of molar teeth, with curvature angles ranging between 50 and 70, were prepared with HyFlex CM and EDM (n = 32 in each group). Quantitative and qualitative analyses of the files' surface deformation were performed by using three-dimensional optical profilometry before and after root canal preparation. The data were analyzed with the Student t test at the 5% significant level by using SPSS 21.0 software. Results: In the HyFlex EDM group, the qualitative evaluation revealed the presence of cracks and microcavities after use of the file for root canal preparation, whereas only minor surface deformation was observed in the HyFlex CM group. The average roughness, root mean square roughness, and peak to valley height values of the HyFlex EDM group were significantly higher than those of the HyFlex CM group before and after root canal preparation (P <.05). The surface roughness values were statistically significantly increased in the HyFlex CM group after root canal preparation (P <.05). In contrast, the increase in the HyFlex EDM group was not statistically significant (P>.5). Conclusions: Within the limitations of the present study, the HyFlex.CM files showed significantly higher surface alterations compared with the Hy Flex EDM files after the preparation of severely curved root canals.