We report a two-stage mechanism of formation of the two-dimensional surperlattices in colloidal gold nanoparticles. The first stage is the formation and growth of holes. When the film is thinner than the "pancake" thickness and because the solvent volatility holes nucleate and grow, the dry solid surface is exposed. The second stage corresponds to the reorganization of the colloids in the impacted areas between several holes, in which the particles gathering along the rims order due to the van der Waals-type attraction between colloids and the confinement by the length of dodecanethiol. Then at a compromised distance and perfect position giving the minimum free energy, ordering occurs in small domains along the boundary of the hole. When the ordered domains become closer because of the hole growth, they rotate at certain angles and the further ordering appears.