To better understand the process of Probe Mediated Deposition (PMD), or Dip-Pen Nanolithography (DPN), we have studied the transport of an amphiphilic molecule, mercaptohexadecanoic acid (MHA), from the tip of an atomic force microscope (AFM) onto a gold substrate. The process was studied as a function of relative humidity (RH), total elapsed patterning time, and procedure for coating the AFM tip with MHA. Molecular transport is strongly dependent on the conditions of the AFM tip, such as prior cleaning techniques, and whether MHA was deposited dry onto the AFM tip, or from a solution. The transport rate of MHA decreases in a roughly exponential manner over about one hour to a rate that is less than a fourth that of the original transport rate. While the molecular transport rate was independent of RH for 52% RH or less, increasing the RH to 70% about doubled the transport rate, and at 98% RH an increase of about 500% was observed. Our data suggest that the MHA is mobile in the absence of a water meniscus, supporting a dual transport mechanism, whereby at low RH, thermal diffusion drives the "dry deposition" of MHA. As RH increases above ∼52%, there is sufficient water present at the tip-substrate interface for aqueous transport of solvated MHA to augment the transport rate.