<jats:title>Abstract</jats:title><jats:p>Fullerene nanostructures are well known for their unique morphology, physical and mechanical properties. The thermal stability of fullerene nanostructures, such as their sublimation at high temperature is also very important for studying their structures and applications. In this work, We observed fullerene nanowhiskers (FNWs) <jats:italic>in situ</jats:italic> with scanning helium ion microscopy (HIM) at elevated temperatures. The FNWs exhibited different stabilities with different thermal histories during the observation. The pristine FNWs were decomposed at the temperatures higher than 300 °C in a vacuum environment. Other FNWs were protected from decomposition with an amorphous carbon (<jats:italic>a</jats:italic>C) film deposited on the surface. Based on high spacial resolution, <jats:italic>a</jats:italic>C film with periodic structure was deposited by helium ion beam induced deposition (IBID) on the surface of FNWs. Annealed at the high temperature, the fullerene molecules were selectively sublimated from the FNWs. The periodic structure was formed on the surface of FNWs and observed by HIM. Monte Carlo simulation and Raman characterization proved that the morphology of the FNWs was changed by helium IBID at high temperature. This work provides a new method of fabricating artificial structure on the surface of FNWs with periodic <jats:italic>a</jats:italic>C film as a mask.</jats:p>