As our understanding of human diseases grows, so does our need to understand functions and pathways on a proteomic level. Protein arrays are a way of analyzing proteins and pathways within single molecule detection. A new concept of fabricating protein arrays based on self assembly of protein/gold nanoparticle conjugates onto nanometer patterns formed by e-beam lithography. Hydrophilic gold nanoparticles (AuNPs) are formed using the Brust-Schiffrin method without stabilizer, and are exposed to a model hydrophobic surface with hydrophilic patterns etched within. The AuNPs bind to the exposed hydrophilic surfaces, while the hydrophobic surfaces repel the gold. This method can be used to bind different proteins to specific size AuNPs, which in turn, when serially added to nanometer patterns, will self assemble onto their respective sized patterns.