Aim: this study was conducted to evaluate and compare the amount of apically extruded debris and canal wall cleanliness using different Ni-Ti instruments (ProTaper file F2, Twisted File 25 and Reciproc R 25) used in continuous rotation and reciprocating motion, in round and oval root canals. Materials and methods: One hundred twenty extracted single rooted teeth were divided into two groups according to the cross section; 60 round and 60 oval cross section. Each group was subdivided into three subgroups according to the file system (20 ProTaper, 20 Twisted File and 20 Reciproc). Each subgroup was further divided into two divisions according to the motion used (10 rotation and 10 reciprocation). Teeth were mounted in glass vials through holes in the rubber stoppers. The glass vials were weighed before instrumentation. Root canal preparation was performed according to its assigned system according to the manufacturer's instructions, and distilled water was used as root canal irrigant. After instrumentation, the amount of apically extruded debris was evaluated by weighing the samples on the microbalance. Thereafter, roots were longitudinally divided for evaluation of smear layer by Scanning Electron Microscope SEM. The data were tabulated and subjected to statistical analysis. Results: Reciprocating motion extruded more debris than continuous rotation motion. SEM examination revealed greater amount of smear layer in the oval cross section canal than round cross section canal.