This article describes novel phase-separation behavior by a binary mixture of alkanethiols when deposited onto a gold surface using micro-and nanodeposition tools, such as microcontact printing (mu CP) and dip-pen nanolithography (DPN). This behavior is significantly different than that observed in the bulk. We demonstrate this behavior using three model compounds: 16-mercaptohexaclecanoic acid (MHA), 1-octadecanethiol (ODT), and CF3(CF2)(11)(CH2)(2)SH (PFT). The identity of the resulting segregated structure is confirmed by lateral force microscopy (LFM) and by selective metal-organic coordination chemistry. Importantly, this phenomenon can be exploited to print sub-100 nm wide alkanethiol lines via conventional mu CP and to form sub-15 nm features using DPN, which is below the ultimate resolution of both these techniques. We also demonstrate that these nanopatterned materials can serve as templates for constructing more complex architectures.