Ellipsometry was used to quantify adsorption and tapping mode atomic force microscopy to study surface aggregation of human serum albumin (HSA), immunoglobulin G (Igc), and fibrinogen (Fib) adsorbed from aqueous solutions onto methylated silicon surfaces. After exposure to air the protein monolayers were spontaneously restructured, exposing disorganized areas with heterogeneity depending on the degree of surface methylation. The aggregation patterns also depended on some properties of the adsorbed protein (such as the number of contact points with the surface), but seemed to be almost independent of the adsorption time. The results indicate that aggregates were formed due to lateral reorganization on the adsorbed layer at the air-liquid interface during the drying process. The interpretation is that the heterogeneous structures result from a thermodynamically driven interaction between the hydrophobic surface and the similarly hydrophobic air. The main conclusion that can be extracted from this work is that fibrinogen (hydrophobic and large protein) interacts more irreversibly with the silicon surfaces than IgG, and much more so than HSA, which is less hydrophobic and smaller than fibrinogen.