Despite significant improvements of resin-composite in dentistry, when used as a restorative material, the main clinical reasons for failure are fracture and secondary caries. The quality of the dentine collagen in adhesive procedures is a critical aspect and affects the restorations longevity. Scarce evidence of the bonding agents effects on collagen at a nanometre scale and a lack of standardisation on the evaluation of surface roughness applied to dental materials are found in the scientific literature. Therefore, the aims of this study were i) to identify the most appropriate model for the study of collagen interactions with bonding agents, ii) to use this model to evaluate nano-scale morphological and electrical changes as consequence of bonding procedures, and iii) to determine the optimal area to assess roughness of resin-composite surfaces. Topographic and surface potential maps were obtained from collagen samples seeded on silicon wafer using advanced imaging techniques: Atomic Force Microscopy (AFM) and Kelvin Probe Force microscopy (KPFM). The samples were then divided in 5 groups of 8 specimens and submitted to the effects of dental chemical agents (citric acid, phosphoric acid, phosphoric acid/chlorhexidine, chlorhexidine, HEMA/TEGDMA). After each agent, the same area of the fibrils was reassessed. Important reductions in height and electrical surface potential were detected. Therefore, it was concluded that chemical agents induce changes in the structure of collagen type I. Moreover, topographic maps at different dimensions were obtained from polished and brushed samples from three different resin-composites using AFM. Using Matlab routines, arithmetical mean height (Sa), root mean square height (Sq) and maximum height (Sz) were obtained at incremental size areas. It was observed a non-linear increase of surface roughness at higher dimensions. These observations suggest that to successfully characterise surface roughness of dental materials is essential measuring and report Sa, Sq and Sz at both, small and large areas and to standardise procedures.