Nanofabrication using arrays of modified atomic force microscopy (AFM) tips can drastically reduce feature sizes and increase data storage densities. Additionally, AFM experiments are valuable tools for characterizing the tribological properties of surfaces. In order to maximize the potential of nanofabrication techniques, it is necessary to understand fully the interactions between AFM tips and substrates, particularly when the latter is compliant and more damage-prone. To address this issue, we have carried out extensive molecular dynamics simulations of the nanotribological properties of self-assembled alkylsilane monolayers (SAMs) on amorphous silica with a realistic model of an AFM tip. Our simulations demonstrate that for fully physisorbed SAMs, even low load contacts can damage the SAM and cause material transfer to the probe tip. This effect, which is commonly ignored, can have a strong effect on the interpretation of experimental measurements. Partial chemisorption of the SAM lowers, but does not remove the possibility of damage.