The paper describes a methodology of applying X-ray computed tomography (CT) in studying textural–morphological characteristics of sulfide-bearing ultramafic rocks from the Yoko-Dovyren layered massif in the northern Baikal area, Buryatia, Russia. The dunites are used to illustrate the applicability of a reliable technique for distinguishing between grains of sulfides and spinel. The technique enables obtaining statistical characteristics of the 3D distribution and size of the mineral phases. The method of 3D reconstructions is demonstrated to be applicable at very low concentrations of sulfides: no than 0.1–0.2 vol %. Differences between 3D models are determined for sulfide segregations of different size, in some instances with features of their orientation suggesting the direction of percolation and accumulation of the sulfide liquids. These data are consistent with the morphology of the largest sulfide segregations, whose concave parts adjoin the surface of the cumulus olivine and simultaneously grow into grains of the poikilitic plagioclase. Detailed information of these features is useful to identify fingerprints of infiltration and concentration of protosulfide liquids in highly crystallized cumulate systems.