The reaction of 5-40 eV O+ and Ne+ ions with alkanethiolate and semifluorinated alkanethiolate self-assembled monolayers (SAMs) is studied under ultrahigh vacuum (UHV) conditions. Whereas Ne+ simply sputters fragments from the surface, O+ can also abstract surface atoms and break C-C bonds in both the hydrocarbon and fluorocarbon SAM chains. Isotopic labeling experiments reveal that O+ initially abstracts hydrogen atoms from the outermost two carbon atoms on an alkanethiolate SAM chain. However, the position of the isotopic label quickly becomes scrambled along the chain as the SAM is damaged through continuous ion bombardment. Scanning tunneling microscopy (STM) monitors changes in the SAM conformational structure at various stages during 5 eV ion bombardment. STM images indicate that O+ reacts less efficiently with dodecanethiolate molecules packed internally within a structural domain than it does with molecules adsorbed at domain boundaries or near defect sites. STM images recorded after Ne+ bombardment suggest that Ne+ attacks the SAM exclusively near the domain boundaries. Taken collectively, these experiments advance our understanding of the degradation pathways suffered by polymeric satellite materials in the low-earth orbit (LEO) space environment.