The present study, aimed to evaluate the surface topography of two rotary NiTi file systems: the Protaper Universal System (Dentsply) and the Liberator system (Miltex). And study the effect of repeated use on their surfaces and compare between them.The presence or absence of twelve defects were checked on every millimeter of the file surfaces circumferentially. Inspection of all files was done first under stereomicroscope for detection of macroscopic defects. Then, for detection of microscopic surface defects, Field Emission Scanning Electron Microscope was used with a magnification range between 250x to 2000x. Scoring the results for surface defects was done by studying the photomicrographs obtained by SEM. Scanning the files before use showed that all files suffered from all types of surface defects evaluated in this study but with different incidence rates. The presence of surface defects suggests that the manufacturing, packaging and handling procedures for all brands of files are far from ideal.After one canal instrumentation, the results showed changes in the incidence of most surface defects but not all changes were statistically significant for both the liberator and the Protaper systems. The same thing happened after instrumentation of six canals but the types of defects that were significantly changed were greater.Statistical analysis also showed that Liberator files experienced a significant change on the incidence of more types of surface defects than the Protaper Universal Files both after instrumentation of one canal and again after six canals.