It has been widely known since the Industrial Revolution that adding small amount of carbon to many metals can improve their materials properties. Recently the same metals have been found to be the catalysts for synthesizing carbon nanotubes, a new form of carbon. It has been speculated that the metal catalyst may need to be comparable in size compared to the diameter of the nanotube in order to serve as the nucleation site or the ‘root’, but the exact role of the catalyst is unclear. By studying deposition of small carbon clusters on Mo surface (a known nanotube catalyst), we observed the formation and evolution of ordered arrays of molybdenum carbide nanocrystals (i.e. carbide superlattices) on Mo (111) surface [Tsui & Ryan, Phys. Rev. Lett. 89, 015503 (2002); also J. Nanosci. Tech. (in press)]. The self-organization of the carbide nanocrystal arrays is determined to be energetically driven, such that the crystalline lattice mismatch between carbide and Mo host determines the size and spacing of the array, as illustrated in a below. The carbide nanocrystals appear to be the ‘roots’ for the carbon precipitates, as shown in STM images below (b and c), from which carbon nanotube ‘seedlings’ can nucleate. This mechanism indicates that arrays of carbon nanotubes can be grown from large catalysts and it may open new opportunities for controlling carbon nanotube synthesis and for device applications.