To evaluate and compare the amount of smear layer & debris retained in the root canal after using SAF and PTN rotary files using SEM. Fourty–eight human permanent mandibular first molar were divided into two in which SAF system & PTN rotary files were used for instrumentation and subdivided into three groups where first group specimens were irrigated with normal saline, second group with 3% sodium hypochlorite and 17% EDTA & third group with 3% sodium hypochlorite and examined under SEM. Collected data was statistically analyzed. When 3% sodium hypochlorite & 17% EDTA were used as irrigants, SAF had shown significantly less smear layer retained compared to PTN on overall comparison as well as in middle third samples in subgroup comparison. Smear layer and debris retained after the biomechanical preparation with SAF was less compared to PTN rotary files along with different irrigants used.