Introduction/Objective Irrigation has an important role in root canal cleaning and its efficiency depends on the type of irrigants, the amount, the technique and the irrigation protocol. The aim of this work was to estimate the efficiency of cleaning of the canal walls by using scanning electron microscope analysis after the instrumentation by rotary NiTi instruments with the use of three different irrigation solutions and two final irrigation protocols. Methods Sixty extracted human incisors were divided into two groups after the rotary instrumentation with the iRace instruments. In both groups, the same amount (1.5 ml) of three solutions (2% sodium hypochlorite solution, 2% chlorhexidine solution, and 10% citric acid solution) and total final irrigation time (90 seconds) was the same. The final irrigation in the first group was accomplished using the technique of continuous irrigation and in the second group it was done using the intermittent protocol. The roots were cut longitudinally and analyzed by thirds (coronal, middle, and apical) on a scanning electron microscope (JSM 6460LV, JEOL Ltd., Tokyo, Japan) with 1,000× magnification. Results The most efficient cleaning of the root canal walls in both groups was seen after the use of citric acid with the intermittent protocol of the final irrigation (90.7% clean walls), while the least efficient was the final irrigation by chlorhexidine with continuous irrigation (80.3%). The most efficient cleaning of the canal walls in both groups was observed in the coronal third and the largest amount of the smear layer in the apical third. Conclusion The most efficient cleaning of the canal was achieved by the use of citric acid and the intermittent protocol of the final irrigation. In all tested solutions, the intermittent protocol of irrigation was more efficient than continuous irrigation.