Electron stimulated desorption of neutral molecular fragments is used to study degradation of ordered organic thin films under low-energy (0-18 eV) electron impact, and total electron doses ranging between 180-550 muC/cm(2). Different saturated linear thiols HS(CH2)(n)X (n=2 or 15, and X=CH3 or COOH) are adsorbed from solution onto a gold surface to produce a self-assembled monolayer (SAM). Here, we present yield function measurements for electron stimulated desorption of moities such as H-2, CH3, CH3CH2, CH3CH2CH2, CO, and CO2 from such thin chemisorbed films. For CH3-terminated SAMs, neutral fragment desorption thresholds lie between 5-7 eV, whereas for COOH-terminated SAMs, desorption thresholds as low as 0.2 and 3-5 eV are observed. The results suggest that the incident electrons interact with functional groups localized at the film-vacuum interface, which then leads to predominantly methyl group C-H, and C-COOH bond cleavage. In addition to nonresonant degradation mechanisms, which vary monotonically from threshold with increasing incident electron energy, structures in the neutral fragment desorption yield functions are related to resonant electron attachment. Particularly for Au-S(CH2)(15)COOH monolayers, this mechanism leads to a desorption peak of CO fragments at incident electron energies near 1.0 eV. (C) 2003 American Institute of Physics.