Here, 5 nm Ag nanocrystals are deposited, using the same procedure, on various substrates differing by their rms roughness, wetting properties and nanoparticle-substrate interactions leading, consequently, to different nanocrystal orderings. Theoretical calculations are carried out to understand how these parameters influence the size of the nanocrystal organizations on the substrate surface. When these nanocrystal arrays are subjected to an oxygen plasma treatment, the nanocrystals perfectly assembled in hexagonal networks remain intact, while the nanocrystals that are not well-packed coalesce to form larger particles independently on the used substrate. This phenomenon is observed on the entire substrate surface. This procedure gives an innovative way of using oxygen plasma generated by the reactive ion etching technique, as a new method to reveal defects in 2D Ag nanocrystal self-assemblies.