The aim of this study was to evaluate six files on the pericervical dentin (PCD) and the smallest dentin thickness zones (SDTZ) in mesial root canals of mandibular molars. Sixty mandibular molars with two mesial canals and Vertucci configuration were aleatory allocated in 6 experimental groups of 10 molars and 20 root canals. Specimens were scanned before instrumentation using the SkyScan 1275 (Bruker microCT, Kontich, Belgium). Group 1 was treated with WaveOne Gold (WG), group 2 with Reciproc Blue (RB), group 3 with TRUShape (TS), group 4 with XP-endo Shaper (XP), group 5 with iRace (IR), and group 6 with TruNatomy (TN). After instrumentation, the molars were scanned again and the images recorded were reconstructed with the NRecon v.1.7 (Bruker micro-CT) and analyzed with CTAn v.1.20.8 software (Bruker micro-CT) quantifying the changes produced in the surface, volume, structure thickness, SMI, and centroids at the Pericervical Dentin area of the root canals (PCD) located from the root canal orifices at the floor of the pulp chamber to 4 mm in the apical direction, and the changes in the Smallest Dentin Thickness Zones (SDTZ) located (from the furcation to 4 mm and 7 mm in the apical direction. The data obtained were compared using Wilcoxon and ANOVA with a 5% significance level. XP and TN were similar in all the parameters (P >.05) at the PCD, but TN showed significant differences from WG, RB, TS, and IR (P <.05), while XP showed significant differences from WG (P <.05) in volume, surface, and structure thickness. Regarding the changes in the SDTZ, the amount of dentin removed was similar between the groups in both canals at the middle 1/3, at the cervical 1/3 for MB canals, and in ML canals for RB, TS, XP, IR, and TN (P>.05). The action of WG was significantly different from that of XP and TN in the cervical 1/3 of the ML canal (P <.05). XP and TN rotatory files with small taper and volume maintained better with minor changes at the PCD and SDTZ, while WG reciprocation file produced the largest change. All the files were maintained centered at the PCD, and their performances were safe with a minimal thickness higher 0.5 mm at the SDTZ, and without risk of perforation. No clinical trials were indicated in this study. The choice of endodontic files is a relevant factor in the conservative performance of root canal treatments.