Utilising self-assembled monolayers (SAMs) to achieve area-selective atomic layer deposition (AS-ALD) as an approach to bottom-up nanofabrication has recently gained significant attention from the nanoelectronics in- dustry. With the continued downscaling of feature sizes, top-down processing can no longer reach the chal- lenging demands of the industry which requires conformal coating of high aspect ratio vias and a reduction in misalignment errors in multi-layered devices. In this work we attempt to imitate the effects of the ALD oxidation pulse experienced by the SAMs during the AS-ALD process by exposing two SAMs of different chain lengths and different functional groups, (3-trimethoxysilylpropyl)diethylenetriamine (DETA) and octadecyltrimethoxysilane (OTMS), to numerous controlled in-vacuo atomic oxygen exposures with subsequent characterisation by X-ray photoelectron spectroscopy (XPS). We monitor the sequential removal of the deposited monolayers with each successive atomic oxygen exposure for both SAMs. The etch rate is observed to be distinct for the different SAMs, the amino-terminated short chain DETA SAM reveals a linear etch rate while the longer chain OTMS SAM reveals an exponential etch rate. The results presented provide some insights into what characteristics are important for choosing the correct SAM for AS-ALD applications.