In this study, we compared the ex vivo removal capacity of two endodontic rotary techniques and determined whether there was a significant quantitative difference in residual material when comparing root thirds. Forty extracted molars were used. The palatal roots were selected, and the canals were prepared using a step-back technique and filled using a lateral condensation technique with gutta-percha points and Endofill sealer. After two weeks of storage in a 0.9% saline solution at 37°C in an oven, the specimens were divided into 2 groups of 20, with group 1 samples subjected to Gates-Glidden drills and group 2 samples subjected to the ProTaper retreatment System. Hedstroem files and eucalyptol solvent were used in both groups to complete the removal procedure. Then, the roots thirds were radiographed and the images were submitted to the NIH ImageJ program to measure the residual filling material in mm. Each root third was related to the total area of the root canals. The data were analyzed using Student's t test. There was a statistically significant difference between the two techniques as more filling material was removed by technique 2 (ProTaper) than technique 1 (Gates-Glidden drills, p < 0.05). The apical third had a greater amount of residual filling material than the cervical and middle thirds, and the difference was statistically significant (p < 0.05). None of the selected techniques removed all filling material, and the material was most difficult to remove from the apical third. The ProTaper files removed more material than the Gates-Glidden drills.