AIM: To evaluate the efficacy of the R-Endo rotary nickel titanium instrumentation system and hand instrumentation to remove gutta-percha or Resilon from root canals. METHODOLOGY: Eighty single-rooted teeth with straight canals were selected, the pulp chamber was opened, and the canals prepared to a size 30, 0.04 taper. The teeth were divided randomly into two groups of 40 each for root filling with gutta-percha + MMSeal sealer or Resilon + RealSeal sealer. After storage, each group was divided into two subgroups, and material was removed with Hedström files or with R-Endo instrumentation. Times to reach the working length and to eliminate filling material were recorded. Root canal walls were examined using scanning electron microscope to evaluate material remnants on each third. The presence of material was measured according to a score scale. The Student's t-test was used to determine significant differences between mean values of time and remaining material (P < 0.05). RESULTS: No significant differences occurred between thirds, material or removal technique regarding remaining filling debris (P > 0.05). However, times to reach the working length and for removal of filling were lower with R-Endo than with Hedström files (P < 0.0001). CONCLUSIONS: Both instrumentation techniques left filling material inside the root canal and mainly in the apical third. There was no difference between the instrumentation techniques.