Highly organized monolayers formed from the self-assembly of octadecyl derivatives on oxide-covered Si and Ti substrates have been exposed to electron beam impact under typical conditions used in lithographic patterning. A combination of X-ray photoelectron spectroscopy, ellipsometry, infrared spectroscopy, and liquid drop contact angle measurements show that the major effect of irradiation is the loss of H, via cleavage of C-H bonds, to form a carbonaceous residue with a surface containing oxygenated functional groups.