The morphological stability of organic nanowires over time and under thermal load is of major importance for their use in any device. In this study the growth and stability of organic nanowires from a naphthyl end-capped thiophene grown by organic molecular beam deposition is investigated via atomic force microscopy (AFM). Aging experiments under ambient conditions already show substantial morphological changes. Nanoscopic organic clusters, which initially coexist with the nanowires, vanish within hours. Thermal annealing of nanowire samples leads to even more pronounced morphology changes, such as a strong decrease in nanowire number density, a strong increase in nanowire height, and the formation of new types of crystallites. This happens even before sublimation of organic material starts. These experiments also shine new light on the formation process of the nanowires.