While stem cells in culture have been predominately controlled through the addition of soluble factors to the media, the impact of the extracellular matrix on stem cell renewal and differentiation has recently come to the forefront. In vivo, cells adhere and respond to cues that are on the nanoscale, thus the presentation of extracellular matrix components on this scale is critical to mimicking the in vivo environment. We have developed a highly flexible nanopatterning technique, employing protein and peptide reactive polymers and electron beam lithography, which can be utilized for studying matrix effects on stem cell renewal and differentiation.