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Objective. A scanning electron microscope (SEM) is a popular tool for investigating the root canal surface to visualize dentinal tubules, the smear layer and various root canal filling materials in endodontics. Most of the SEM micrographs taken in endodontic research are in secondary electrons (SE) mode, in which the topographic view of a subject can be demonstrated without giving any information about the real structure. Back-scattered electron (BSE) images are also used, which reveal some information about the internal structure while providing no topographic details. The aim of this study was to investigate the possibility of using back-scattered (BSE) and secondary electron (SE) mode of scanning electron microscopy (SEM) together for obtaining detailed information about biomaterials in relation to dental structures. Materials and methods. Mesiobuccal roots of four permanent maxillary molars were cleaned and shaped with rotary instruments. Two samples were obturated with gutta-percha and sealer. After 2 weeks, gutta-perch was removed using rotary instruments and chloroform. In the other phase of the study, white mineral trioxide aggregate was mixed and packed into five glass tubes and exposed to blood, deionized water, synthetic tissue fluid and egg white. All the samples were prepared for visualization under SE and BSE modes of SEM to observe the characteristics of material remnants and surface structures. Results. BSE mode illustrated different grey scale views which made it possible to differentiate dentin chips from filling material remnants on the surface of root canal dentin. In addition, SE mode focused on image topography, while a BSE detector showed new texture formation on the surface of white mineral trioxide aggregate exposed to proteinaceous fluids such as blood or egg white. Conclusions. Mapping BSE and SE micrographs helped us to better understand the structure of materials on the surface of root canal dentin and MTA. Moreover, analysis of structure of materials on the surface of root canal dentine and MTA can be performed better by mapping of BSE and SE micrographs. [ABSTRACT FROM AUTHOR]