The thermal transformations of as-deposited Fe(CO)(5) films adsorbed on Au(111)/mica and C-4, C-8, C-12, and C-16 self-assembled methyl-terminated monolayer organic surfaces have been studied using infrared spectroscopy to probe how the physical restructuring influences the sensitivity of these systems to low-energy electron beams. A companion publication shows that the as-deposited monolayers are composed of molecules physisorbed with one axial and two equatorial carbonyl groups directed toward the substrate; subsequent layers are preferentially oriented with the C-3 molecular axis aligned perpendicular to the substrate (i.e., one axial carbonyl group directed toward the substrate). In this work, we show that the as-deposited films are structurally unstable above 125 K on Au(111)/mica surfaces and above 100 K on the organic self-assembled monolayers. Above these thresholds, the layered structures transform into three-dimensional aggregates, implying strongly nonwetting behavior for Fe(CO)(5) on each of these substrates; molecular desorption from this aggregate structure takes place between 140 and 160 K. The irreversibility of this temperature-induced transformation demonstrates that the as-deposited layered films do not represent a thermodynamically well-defined phase; this key feature of the as-deposited films is believed to be the cause of the discrepancies in previous attempts to understand Fe(CO)(5)/surface structures based on infrared results. Moreover, the thermally induced transformation to 3D aggregate structures is shown to decrease the apparent sensitivity of the adsorbed Fe(CO)(5) to low-energy electron-induced decarbonylation (0-10 eV) by over 3 orders of magnitude.