Here, we describe the effect of writing speed in dip pen nanolithography on the morphology (height and density) of self-assembled monolayers of alkanethiols on gold surfaces. The analysis of atomic force microscopy images of written monolayers shows that molecules assemble according to a nucleation and growth mechanism. Slow writing speeds lead to dense monolayers that can be used either to direct the self-assembly of metal nanoparticles or as masks for selective etching of conductive gold nanowires.