We describe a new combinatorial method for studying the exchange between solution adsorbates and nanoscale features within libraries generated via dip-pen nanolithography. Four different compounds, 1-octadecanethiol, 16-mercaptohexadecanoic acid, ferrocene (11-mercaptoundecyl), and ferrocene (11-mercapto-1-oxoundecyl), are studied on amorphous and single-crystal gold substrates. This series of adsorbates allows us to compare the exchange properties of patterns of nanoscale features as a function of composition, feature size, and type of underlying substrate. Moreover, these properties can be compared and contrasted with bulk SAM properties. The novel strategy provides not only a method for initiating site-specific exchange processes but also a way of extracting kinetic information about the rate of such processes in situ.