MATERIALS AND METHODS: Eighty-four single rooted human teeth were randomly divided into 7 groups, 12 cases each, and canals were instrumented with Mtwo rotary systems. 5.25% sodium hypochlorite, Smear Clear and 17% EDTA were used for irrigation of the canal during and/ or after instrumentation. After completion of instrumentation, all canals were dried with paper points and prepared to examine by scanning electron microscope. All SEM photomicrographs were scored at the coronal, middle and apical thirds of canals in each group. The data were statistically analyzed using Mann-Whitney and Kruskal-Wallis tests. RESULTS: In the group irrigated with Smear Clear alone, the coronal thirds of the canals were significantly cleaner than middle thirds (P= 0.013) and apical thirds (P=0.028). There were less smear layer in the coronal thirds compared to apical thirds (P=0.047) in the group irrigated with Smear Clear and NaOCl alternately .There were significantly more smear layer in the apical thirds compared to coronal thirds (P<0.001) and middle thirds (P=0.007) in the group that Smear Clear and NaOCl were used as final irrigations. There was not any significant difference between three-thirds of the canals in other groups. Comparison of the all groups showed a statistically significant difference (P<0.001) in the amount of debris and smear layer remaining at all three levels of the canals. CONCLUSION: The findings of this study suggested that a final rinsing by combination of a chelating agent like EDTA or Smear Clear and NaOCl is necessary to obtain favorable clean wall of root canals.