The aim of this study was to evaluate & compare the cleaning efficacy of teeth instrumented with two different rotary instrumentation systems. The two file systems used in this study were Protaper Next and K3 File System. 66 extracted, single-rooted human mandibular canine teeth were selected and divided into 2 groups of 30 teeth each. 6 teeth were used as negative controls. In group 1, teeth were prepared with Protaper Next File system while in group 2 teeth were prepared with K3 File System respectively. Teeth were longitudinally sectioned and each half was further divided into three parts that is the coronal, middle and apical third and each third was evaluated at a magnification of 40X under stereomicroscope. SEM evaluation of the same was done under 500X. Based on the stereomicroscopic analysis ofspecimens, it can be concluded that in the apical third of root canal system cleaning efficacy was significantly higher for Protaper Next and K3 file system as compared to Hero Shaper file system while based on the SEM analysis of specimens, it can be concludedthat in the coronal, middle and apical third of root canal system, cleaning efficacy was significantly higher for the K3 file system