Collagen is a ubiquitous component of the extracellular matrix environment, and numerous studies have been devoted toward the development of collagen-based tissue scaffolds. These efforts have been primarily focused on synthetic collagenous materials made from purified collagen. In this article, we present a preliminary study toward the development of a technique that can result in a tissue-derived collagen scaffold. The tissue-derived collagenous matrix was isolated from the retinal Bruch's membrane, and dip pen nanolithography was investigated as a mean to modify the collagenous surface. Characterization experiments of the collagenous surface indicate a fairly hydrophobic surface. Minimal swelling (<7%) of the collagen fibers was observed under elevated humidity conditions with negligible rearrangement of the surface. The hydrophobicity and roughness of the surface can pose a barrier for the deposition of molecules via scanning probe lithography. However, deposition of poly(glutamic acid) and polyarginine onto the surface could be achieved under high contact force and elevated relative humidity conditions (above 55%). Under these conditions, the deposition of the polypeptides occurred through molecular deposition with no observable molecular diffusion. On the other hand, the addition of 0.1% (v/v) Tween-20 surfactant to the inking solution facilitated diffusion of polypeptide inks by increasing the wettability of the collagenous surface. As such, deposition of molecule can be observed under lower contact force at ambient relative humidity (37−40%).