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.