Predicting how proteins fold and adsorb onto surfaces is a complex problem of strong relevance to the health and environmental sectors. In this work, two nano-patterning techniques, namely focused ion beam (FIB) milling and atomic force microscopy (AFM) nanoindentation were used to develop hydrogenated amorphous carbon (a-C:H) model surfaces with similar nano-topography but different local composition. On the un-patterned surfaces, bovine plasma fibrinogen (BPF) resulted in a thicker and rougher adsorbed film than bovine serum albumin (BSA), although FTIR analysis indicated that, the secondary structure of the proteins changed similarly, with an increase of the β-sheet component (+ 27% and + 34% for BSA and BPF, respectively). AFM analysis on the FIB-patterned surfaces indicates that patterning can modify specific protein adsorption behaviors. Moreover, the patterns were compared by imaging the AFM tip/surface adhesive force for BSA adsorbed on either AFM tips or patterned surfaces. The results show an electrostatic interaction between the implanted Ga⁺ and BSA surface, modifying the adsorption behavior and the adhesive force. Modelling this interaction gave an estimate of the surface charge per protein, a significantly lower value than in dilute solution (− 1.8e instead of -18e). This finding is indicative of protein misfolding, as detected in the FTIR analysis.