We develop self-organisation processes for the fabrication of 2D arrays of Si and Ge quantum dots. The processes make use of the dewetting phenomenon which involves the transformation of a 2D thin film into an array of isolated 3D islands through a morphological instability. We show that self-organization of monodisperse ultra-small nanocrystals (NCs) into large scale patterns with ad hoc features can be created via heterogeneous dewetting. The process involves dewetting of thin films nanopatterned by electron beam lithography (EBL) or liquid metal alloy source focused ion beam (LMAIS-FIB). Heterogeneous dewetting is initiated at the edges of the patterns. It provokes the retraction of the thin film following the kinetics of surface diffusion and ends by the formation of faceted monocrystalline NCs regularly positioned. Their geometrical features and lateral arrangements can be tuned by changing the pitch, size, and shape of the patterns. The process developed in this study is adapted to the fabrication of NCs based floating gate memories.