Abstract Ruthenium (Ru) nanofilms (<3 nm) were prepared using tricarbonyl(trimethylenemethane)ruthenium, Ru(TMM)(CO)3 at 230 oC. 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 tunneling junction structure. The results emphasized the difference in carrier transport in Ru nanofilms on Si and SiO2 substrates.