Background: Endodontic treatment objectives comprise eliminating or decreasing bacterial load inside the complex endodontic space. Removing the smear layer and debris becomes mandatory to achieve good three-dimensional (3D) cleaning. Aim: This study assesses the difference in smear layer removal using the 3D cleaning technique and traditional syringe needle irrigation. The 3D cleaning technique includes the ultrasonic activation of intracanal-heated NaOCl. Materials and Methods: Our current study used single-rooted human mandibular premolar teeth to test the earlier-mentioned technique (n = 30). Initially, an endodontic access cavity was performed. Consequently, specimens were randomly distributed into three study groups according to irrigation protocol. The groups were Group 1, where the traditional syringe needle irrigation system was applied; Group 2, where the 3D cleaning technique was performed; and Group 3, in which teeth remained uncleaned as it was regarded as the control group. Once the experiment was completed, the teeth were decoronated at the cementoenamel junction (CEJ) and examined using scanning electron microscopy (SEM). Debris and smear layers were viewed in 1000× magnification and scored. Results: Statistical analysis was performed with a standard statistical software package (SPSS, version 28.0; SPSS IBM, Armonk, NY, USA). Data were analyzed with a nonparametric analysis of variance (Kruskal–Wallis ANOVA) among the groups tested and among the thirds of the canals. The level of significance was set at p < 0.05. A statistically significant (p < 0.05) lower mean smear layer and debris score was observed in both study groups compared to the control group. Group 2 showed better results compared to Group 1. Conclusions: The present study concluded that the 3D cleaning technique is an effective irrigation method for removing debris and smear layers. Future research, such as CLSM (Confocal Laser Scanning Microscopy) and Histological study, should be employed to confirm this study’s conclusion.