Bacterial adhesion to the surface of the adhesive material is an important step in the formation of plaque and enamel demineralization. In order to correlate the material composition to the specific surface roughness of the resin and to the probable more favourable adhesion of bacteria, scanning electron microscopy, combined with focus ion bean micromachining, together with stylus profilometry analysis have been in vitro performed to reveal the structural nature of three orthodontic adhesive resins used for bracket bonding and, above all, to understand how compositional factors can influence specific pivotal properties such as material’s surface roughness and robustness. In particular, we speculated about the morphological features that determine an increase in the bacterial adhesion and we proposed focused ion beam technique as a valuable tool to compare the internal structures of the polymers and to determine the peculiar mechanical properties of the examined adhesive resins.