In this work the directed (replacement lithography) and non-directed replacement of Self-assembled monolayers (SAMs) of various binding groups and structures on different substrates was explored. First, the effect of order in alkanethiol SAMs on gold on the amount of replacement in replacement lithography was explored. It was shown that higher ordering in these SAMs resulted in less amounts of replacement. Attempts were made to explore the use of alkanethiol SAMs on GaAs in replacement lithography, but this was frustrated by difficulties characterizing the initial SAM formed and the stability of the SAM. In another case, non-directed (adventitious) replacement of SAMs comprised from n-alkane thiols and terminal alkynes on gold were explored. These SAMs were subjected to solutions containing ferrocene-terminated thiol, thioacetate and terminal alkyne, respectively. The rate and extent of chemical exchange was monitored by scanning tunneling microscopy (STM). In several cases, a rate constant for exchange could be obtained by fitting to a model for exchange. In each case where this could be accomplished, a different rate model gave the best fit to the data, suggesting that the mechanism of exchange depended on either or both the original SAM and the incoming molecule. In scenarios where the rate of exchange was slow, replacement lithography was accomplished. The extent of exchange by replacement lithography was independent of the ink molecule, suggesting that tip-induced desorption was the limiting factor in this process. Also, the adventitious replacement of SAMs comprised from n-alkane thiols and alkylisonitriles on plantinum was explored. These SAMs were subjected to solutions containing ferrocene-terminated thiol and ferrocene-terminated isonitrile. The rate and extent of chemical exchange was monitored by STM, but the rapid amount of replacement frustrated attempts to study the exchange of these films.