Introduction/Objective The application of nickel-titanium (NiTi) instruments in cleaning and shaping of the root canal system is a standard and a precondition for the success of endodontic treatment. The objective of this study was to use scanning electron microscopy (SEM) analysis in order to examine the efficiency of cleaning the apical third of the root canal system using two different NiTi systems with reciprocating movements. Methods The study included 20 single-rooted teeth (premolars) divided into two groups. In group 1, the canal preparation was realized with a single file UNICONE with reciprocating movements (MEDIN, Inc., Nové Město na Moravě, Czech Republic), and in group 2, with а RECIPROC BLUE instrument with reciprocating movements (VDW GmbH, Munich, Germany). The same quantities of 2% NaOCl solution and 17% EDTA solution were used as irrigation solutions. The samples prepared for SEM analysis of the smear layer in the apical third were evaluated on a scale of 1-5 and at a magnification of 1,000×. Results SEM analysis pointed to mostly clean canal walls in the apical segment in both tested groups. Slightly cleaner walls were observed after the application of the UNICONE file (78%) compared to the samples of the second group, where the instrumentation was realized by the RECIPROC BLUE file (76%), but without statistically significant differences. Conclusion Single-file reciprocating systems do not remove the smear layer completely, but provide efficient cleaning of the apical region of the canal.