MgO nanodots have been deposited and formed on top of the substrate surface. Mg was sputtered to form the MgO nanodots on the single crystal substrates by rf-sputtering method and followed by heat treatment in the oxygen ambient. The deposition and formation of MgO nanodots have been controlled systematically using the process variables such as substrate temperature, sputtering time, and rf-power. As the substrate temperature increased from the room temperature the density of MgO nanodots decreased. The optimal conditions of MgO nanodots formation using the rf-sputtering was investigated and the maximum density of more than $230/{mu}m^2$ on single crystal substrates was obtained when the rf-power of 100 watts was applied for 30 seconds at room temperature. The typical size of MgO nanodots was identified to be <160 nm(diameter) and 4-30nm (height) by atomic force microscopy. The modulated surface morphology was examined through surface images and cross-section analysis and discussed for the artificial pinning sites in the superconducting films.