To evaluate morphological changes of the apical surface after root canal preparation with 1 mm beyond the apical foramen using ProTaper Universal (PTU) files, K3 files and Twisted files (TF), respectively. Seventy teeth with a centered apical foramen and 70 teeth with a deviated apical foramen were included as group A and group B respectively. In each group, 20 teeth were randomly assigned for root canal preparation with PTU, K3 and TF files, respectively; the remaining 10 teeth were used as the control group without any preparation. The apical foramens were examined with scanning electronic microscopy. The foramen integrity damage (FID) and dentin defects (DDs) were noted and compared between different groups. FID and DD were significantly less in Group A. DDs was not found in the control group. Preparation with PTU, K3, and TF files caused FID in 6.67%, 10%, and 3.33% of teeth in the group A, and in 20%, 26.67%, and 10% in Group B, respectively. Preparation with PTU, K3, and TF files caused DD in 6.67%, 6.67%, and 3.33% of teeth in Group A, and in 23.33%, 26.67%, and 6.67% in Group B, respectively. PTU and K3 files produced more DDS than TF files. However, no significant difference was found between groups using PTU and K3 files. Rotary instrumentation caused less damage on the apical surface in foramencentered root canals than foramen-deviated root canals when working beyond the canal length. TF files had a tendency to produce less DDS compared with PTU or K3 files during over-instrumented root canals.