Ruthenium (Ru) nanofilms (<3 nm) were prepared using tricarbonyl(trimethylenemethane)ruthenium, Ru(TMM)(CO)3 at 230 °C. We show that the surface morphology and electrical conductance of Ru nanofilms are substantially different on H:Si(100) and SiO2/Si(100) substrates. Two-dimensional (2D) Ru nanofilms (∼1 nm) were formed on H:Si(100), while thick (∼3 nm) granular Ru films were formed on SiO2 substrate under the same growth conditions, as confirmed by cross-sectional transmission electron microscopy and X-ray photoelectron spectroscopy. Using scanning probe microscopy, the metallic conductance of Ru grains on H:Si(100) substrates was recognized. On ultrathin (1 nm) SiO2/Si(100) substrates, the spatial separation of Ru grains facilitates the single electron tunneling (SET) phenomenon in the double barrier tunnel junction structure. The results emphasized the difference in carrier transport in Ru nanofilms on Si and SiO2 substrates.