SEM analysis of endodontic instruments from a Ni-Ti rotary system was assessed, before and after using them, considering their defects and deformations. Twenty Twisted File®, BioRąCe®, Mtwo®, and EndoWave® instruments were micrographed at 190× magnification. The files were washed and micrographed again to view alterations as to the presence or absence of irregular edges, grooves, microcavities, and scraping. Simulated root canal preparations were performed using these instruments. The instruments were cleaned and received a microscopic analysis after being used five times. After analysis tests were tested using Fisher's exact test and Kappa to evaluate the concordance among examiners. There was a statistically significant difference with respect to deformations between Twisted File® and other instruments (p < 0.05). There was no statistically significant difference in strains between the other groups (p > 0.05). All Twisted File® instruments showed the same defects; however damage were lower than those found in BioRace® and Mtwo®. The Endowave® did not show the same defects. In accordance with the data we conclude that the presence of defects was higher in Twisted File® instruments as the instruments and BioRace® Mtwo® brand, the defect rate was smaller and Endowave® instruments had no defects. Regarding the presence of wear after five uses among the groups all instruments showed changes in their cutting blades.