Bacterial adhesion to the surface of orthodontic materials is an important step in the formation and proliferation of plaque bacteria, which is responsible for enamel demineralization and periodontium pathologies. With the intent of investigating if adhesive resins used for bracket bonding are prone to bacteria colonization, the surface roughness of these materials has been analyzed, combining information with a novel methodology to observe the internal structures of orthodontic composites. Scanning electron microscopy, combined with focus ion bean micromachining and stylus profilometry analyses, were performed to evaluate the compositional factors that can influence specific pivotal properties facilitating the adhesion of bacteria to the surface, such as surface roughness and robustness of three orthodontic adhesive composite resins. To confirm these findings, contact angle measurements and bacteria incubation on resin slide have been performed, evaluating similarities and differences in the final achievement. In particular, the morphological features that determine an increase in the resins surface wettability and influence the bacterial adhesion are the subject of speculation. Finally, the focused ion beam technique has been proposed as a valuable tool to combine information coming from surface roughness with specific the internal structures of the polymers.