We studied the self‐organization (SO) of small‐size (D = 90 nm), medium‐size (220 nm), and large‐size (450 nm) colloidal silica nanoparticles in Langmuir‐Blodgett layers induced by a focused Ga+ ion beam with energy of 30 keV. The ion irradiation induces SO into various types of clusters as the result of particle charging and heating, Coulomb repulsion and motion on the substrate surface, as well as of particle ‐ particle and particle ‐ substrate interaction. These processes show a great difference of the underlying dynamics and of the characteristics of SO pattern, depending on the particle size and on the ion fluence. The two dimensional (2D) pattern of the small‐size particles is transformed into “infinite” chain‐cluster, while the pattern of medium‐size particles is transformed into a number of short separated chain‐clusters. The pattern of large‐size particles is mostly unchanged, but shows particle melting and buckling, which at higher fluences passes into ion beam‐induced sputtering (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)