The phenomenon of surface self-healing in C60-based polymer coatings deposited by ion-beam assisted physical vapor deposition was investigated. Nanoindentation of the coatings led to the formation of a protrusion rather than an indent. This protrusion was accompanied by an abnormal shape of the force-distance curve, where the unloading curve lies above the loading curve due to an additional force applied in pulling the indenter out of the media. The coatings exhibited a nanocomposite structure that was strongly affected by the ratio of C60 ion and C60 molecular beam intensities during deposition. The coatings also demonstrated the dynamic hardness effect, where the effective value of the hardness depends significantly on the indentation speed.