$Y_{2}O_{3}$ nanodots have been deposited on top of the substrate surface using rf-sputtering method. This approach was adopted to be able to modulate the substrate surface with nanodots used as a seed for the flux pinning sites in the superconducting films. The nanodot density of $Y_{2}O_{3}$ was controlled mainly using the deposition time, rf-power, and substrate temperature. $Y_{2}O_{3}$ nanodots with ${sim};50;nm$ in diameter and ${sim};3;nm$ in height were obtained at rf-sputtering time of about 15 seconds using 400 watts of rf-power and $630^{circ}C$ of substrate temperature. As deposition time increased up to about 30 seconds, the interconnected islands of $Y_{2}O_{3}$ nanodots formed, which can be clearly observed with AFM surface image. The substrate surface was covered entirely with $Y_{2}O_{3}$ layer above the deposition time of 60 seconds. The modulated surface morphologies and cross section analysis of deposited $Y_{2}O_{3}$ nanodots at various experimental conditions have been examined using AFM and discussed with respect to the flux pinning sites for the practical application.