The temporal evolution of the morphology of nanoscale-patterned phospholipid thin films on mica and silicon surfaces has been investigated with an atomic force microscope (AFM). The AFM images reveal that nanoscale scratch lines on thin films prepared on mica contract with time and eventually form roundish holes. An elevated sample temperature accelerates this morphological evolution. We model such an evolution based on the interplay of the thin-film surface line tension and the friction between the thin film and the substrate. The results show that the temperature-dependent contraction is governed by the ratio of the friction coefficient and the surface line tension. The friction at the lipid/mica interface decreases to a seventh as the sample temperature rises from 18 to 60 °C. This model is supported by experiments on silicon surfaces, on which contraction of the scratch patterns is limited because of an expected greater interfacial friction.