The aim of this study was to compare the shaping ability of a modified ProTaper Next technique (PTNm) with that of TruNatomy (TN) in lower molars mesial curved canals using micro-computed tomography (Micro-CT). Sixty mesial canals of first mandibular molars were randomly assigned between two groups (n = 30). After canal scouting with K-File #10, glide path and shaping were carried out with TN or PTNm systems. The PTNm sequence consists of ProGlider, followed by ProTaper Next X1 and apical finishing with NiTiFlex #25 up to working length (WL) to ensure adequate apical cleaning. Samples were scanned using micro-CT and pre- and post-shaping volumes were matched to analyse geometric parameters: the volume of removed dentin; the difference of canal surface; centroid shift, minimum and maximum root canal diameters; cross-sectional areas; the ratio of diameter ratios (RDR) and the ratio of cross-sectional areas (RA). Measurements were assessed 2 mm from the apex and in relation to the middle and coronal root canal thirds. Data were analysed using ANOVA (p < 0.05). No statistically significant differences were found between the groups for any parameter at each level of analysis, except for RA at the coronal level (p = 0.037). The PTNm system showed the tendency to enlarge more in the coronal portion with a lower centroid shift at apical level compared with TN sequence (p > 0.05). Both PTNm and TN sequences demonstrated similar maintenance of original anatomy during the shaping of lower molar mesial curved canals.