Modern endodontics has provided significant advancements, particularly in the treatment and retreatment of root canals. However, the complete removal of obturation material during retreatment remains a challenge, especially in the apical third of root canals, where complex anatomy imposes limitations. This study aimed to evaluate the effectiveness of using WaveOne Gold reciprocating instruments of different diameters and kinematics (brushing motion and pecking motion) for removing obturation material from root canals during retreatment, with a particular focus on the apical third. Thirty human maxillary molars with separate roots were selected and divided into four groups. Root canals were prepared and obturated using different WaveOne Gold instruments (Primary and Medium) and then retreated with larger diameter instruments using different kinematics. The removal of obturation material was evaluated through cone beam computed tomography (CBCT). The results were statistically analyzed using ANOVA and logistic regression. Statistical analysis revealed no significant differences between the groups regarding the type of instrument or kinematics applied. Residual obturation material was observed in approximately 60% of the samples, regardless of instrument diameter or kinematics used, indicating that complete removal of obturation material from the apical portion of root canals remains a substantial challenge. The use of larger diameter instruments, such as the WaveOne Gold Medium, and the application of brushing motion kinematics did not prove significantly more effective in removing obturation material compared to smaller diameter instruments. These findings highlight the need to explore new approaches and technologies to optimize obturation material removal, especially in complex anatomical regions like the apical third of root canals.