We report here the first study on the formation of two-dimensional (2D) periodic arrays of nickel metal and Ni-silicide nanodots on Si(111) substrates by the colloidal nanosphere lithography (NSL) and thermal annealing techniques. For the Ni metal nanodot array on Si(111) sample after annealing, NiSi 2 appears to form as the first silicide phase at a temperature as low as 250 °C. From transmission electron microscopy (TEM) and electron diffraction analyses, the NiSi2 nanodots were found to grow epitaxially on the Si(111) surface with the crystallographic relationships NiSi2 || Si and NiSi2(220)|| Si(220). In the higher temperatures annealed samples, many of the epitaxial NiSi2 nanodots were observed to have truncated shapes, and the formation of the faceted structures became more pronounced as the annealing temperature increased. The observed results demonstrate that using the colloidal NSL and heat treatment approaches, it is expected that the investigations of the interfacial reactions of various metal nanodot arrays on Si-based substrates can be achieved.