This article reports the use of dip pen nanolithography (DPN) for the study of adsorption of bovine serum albumin (BSA) proteins on amorphous carbon surfaces; tetrahedral amorphous carbon (t-aC) and silicon doped hydrogenated amorphous carbon (a-C:H:Si). Contact angle study shows that the BSA proteins reduce the contact angle on both carbon materials. We also noticed that the drop volume dependence is consistent with a negative line tension; i.e. due to an attractive protein/surface interaction. The DPN technique was used to write short-spaced (100 nm) BSA line patterns on both samples. We found a line merging effect, stronger in the case of the a-C:H:Si material. We discuss possible contributions from tip blunting, scratching, cross-talk between lever torsion and bending and nano-shaving of the patterns. We conclude that the observed effect is caused in large measure by the diffusion of BSA proteins on the amorphous carbon surfaces. This interpretation of the result is consistent with the contact angle data and AFM force curve analysis indicating larger tip/surface adhesion and spreading for the a-C:H:Si material. We conclude by discussing the advantages and limitations of DPN lithography to study biomolecular adsorption in nanoscale wetting environments.