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Introduction: The study aims to evaluate the effect of apical preparation size on the removal of the smear layer and organic debris from the root canal wall. Methodology: Thirty freshly extracted single-rooted teeth with comparable root canal morphology were selected. Chemo-mechanical preparation of root canals was done with hand K-files up to 20/0.02 and samples were randomly divided into three groups of 10 specimens each, Group-A (control group): Without further chemomechanical preparation; Group-B: Final chemomechanical preparation with rotary nickel-titanium files up to 25/0.04; Group-C: Final chemomechanical preparation with rotary nickel-titanium files up to 30/0.04. Copious irrigation was done with 17% ethylene diamine tetra acetic acid and 5.25% sodium hypochlorite. The data were analyzed via the Mann-Whitney U test with the help of SPSS 17 statistical software. Results: A significant reduction of the smear layer and organic debris was observed when prepared with rotary nickel-titanium files to a final apical size of 30/0.04 compared to the final apical size of 25/0.04 in the apical third. Conclusion:Increasing the size of the apical preparation to 30/0.04 greatly improved the cleanliness of the root canal walls.