Ru nanocolumns were grown on a native oxide covered Si(100) substrate using an oblique angle sputter deposition technique with substrate rotation at room temperature. Scanning tunneling microscopy images of conventional Ru film show the presence of straight columnar features on the film surface, which are very different from the nearly circular features observed on the nanocolumns surface. X-ray diffraction spectra confirm that these nanocolumns have (100) as the preferred orientation instead of the (002) orientation observed for a conventional film. The oxygen to Ru atomic ratio was determined for both the nanocolumns and the conventional film by using X-ray photoelectron spectroscopy. The nanocolumns were observed to incorporate about 6 times more oxygen than the conventional film near the surface region. We argue that the oxygen segregates onto the high-density (002) plane whereas it permeates through comparatively open planes like (100) and (101). The adsorbed oxygen atoms serve as a diffusion barrier for the landing Ru adatoms and inhibit the growth of the (002) plane. This results in the absence of the (002) plane and development of (100) and (101) planes in the nanocolumns. The oxygen plays a decisive role in determining the crystallographic orientation and the feature size/shape over the nanocolumns and conventional film surfaces.