The thermally induced structural changes in Langmuir-Blodgett films of Ca-arachidate with one and nine layer thicknesses and those in self-assembled monolayers of alkanethiols were investigated systematically between 300 and 410 K using near edge x-ray absorption fine structure (NEXAFS) spectroscopy. With increasing temperature the initial strong linear NEXAFS dichroism reflecting the high degree of orientational order within the films decreases continuously and vanishes above 390 K. In addition, the spectra recorded for elevated temperatures (above 400 K) show a peak splitting of the prominent R* resonance at 287.7 eV which is attributed to changes in the electronic structure of the alkane chains caused by thermally induced structural defects, i.e., gauche conformations. The intensity of this new feature increases exponentially with temperature and allows one to extract an energy of 46 kJ/mol (480 meV) for the creation of a gauche conformation in densely packed hydrocarbon films.