||The purpose of this thesis is to investigate the formation mechanisms of metal oxide nanowires such as VO2 and ZnO, their novel structures, interfaces, phase transformation, electrical properties, optical properties and structural modification on these nanowires by the focused-ion beam (FIB) technique. VO2 nanowires fabricated using the thermal evaporation technique show interesting growth phenomena on different substrates. Under certain growth conditions, single crystalline VO2 nanowires may grow along the substrate surfaces which are different from the nanowire growth behavior of other material systems. The morphologies, interface structures and growth direction of these nanowires have been systematically investigated. On the surface of an amorphous silica substrate, all VO2 nanowires grew along the substrate surface without the aid of any metal catalysts. This is due to the strong affinity between the vanadium oxide nanocrystals and silica surfaces. Because the vanadium oxides at the growth tip and the nanowire body had different melting temperatures, and VO2 crystals had a very different thermal expansion coefficient in comparison with silica, the growth tips separated from the nanowires during the cooling down process. Based on our study of the special nanowire tip structures, the growth of VO2 nanowires was interpreted by the oxide-assisted growth mechanism. VO2 undergoes a metal-to-insulator transition (MIT) accompanied by a reversible structure transition from a high temperature tetragonal (T) structure to a low temperature monoclinic (M) structure at 340K. Under the electron-beam irradiation in TEM, the reversible phase transformation process has been observed at atomic level by high-resolution transition electron microscopy. The interface structures and orientation relationships between the tetragonal and monoclinic phases have been identified. For example, after increasing the intensity of the electron beam, the lattice fringes of (1̅ 00) planes of the monoclinic structure were replaced by that of the (011) planes of the tetragonal phase in some thin areas, particularly the areas near the center of the electron beam (higher electron density). The areas of the tetragonal phase grew and showed clear interfaces between these two phases. The reverse transition started in the thick areas or at the edge of the illuminated areas when the intensity of the electron beam was decreased. In this phase transition, the orientation relationships between these two phases were: M//T; M//T; M//T. The interface between the two phases was (010)M//(100)T. On sapphire substrates, single crystalline VO2 nanowires exhibited interesting epitaxial growth phenomena along three equivalent <11̅ 00> directions of the a-planes, c-planes and m-planes. At certain growth temperatures, the VO2 nanowires formed V-shaped twining structures with uniform morphologies and interfaces on the c-planes sapphire substrates. Due to the strong elastic strain at the interfaces, the MIT transition of individual VO2 nanowires grown epitaxially on sapphire substrates displayed distinct electrical hysteresis loops in comparison with those simply dispersed on sapphire substrates. The thermal hysteresis property induced by MIT and accompanied changes of domain structures were characterized by optical microscopy and electrical measurements. The distinct characteristics in the hysteresis loops during the MIT transition were correlated with the nucleation and growth of periodic or random domain structures in the nanowires during heating and cooling processes. Using FIB technology (through an ultra fine Ga ion beam), nano-sized structures can be modified or processed. However, the Ga ion beam also causes damages during nanofabrication. The damages induced by FIB in bulk Si crystals, Si thin films and different metal oxide nanowires have been investigated by high-resolution transmission electron microscopy (HRTEM). ZnO nanowires have been found to be very stable under Ga ion beam bombardment. The possible reasons for the formation of the damage layers in different materials were discussed based on ion-solid interaction theory. Moreover, it has been observed for the first time by cathodoluminescence (CL) spectroscopy at liquid nitrogen temperature that the Ga-ion beam can largely suppressed or eliminate the defect-induced green light emission. While, the Ga beam has nearly no impact to the UV emission from ZnO nanowires. Based on this interesting effect, ZnO nanowires with controllable periodically doped structures have been fabricated which have potential technological applications in nanodevice fabrication.