New materials made of two- and three-dimensional superlattices of nanoparticles exhibit unique collective properties arising from the ordering of the nanoparticles. Here, dodecanethiol-coated silver nanocrystals self-assembled in 2D were subjected to oxygen plasma using the reactive ion etching process. The careful investigation by transmission electronic microscopy (TEM) of the same areas before and after exposure allows one to distinguish two behaviors under plasma treatment, which are determined by the level of ordering of the 2D organizations. Higher ordered self-assemblies remain unchanged, while less ordered organizations coalesce into larger nanocrystals with spheroidal shapes that could be single crystals. Electron energy-loss spectroscopy (EELS) measurements show that there is no oxidation of the silver either on the large coalesced nanocrystals or on the stable self-assemblies. A new intrinsic property, immunity of highly self-ordered nanocrystals provided by the ordering, is reported, and a mechanism of the coalescence is proposed.