In this study, we demonstrate an atomic force microscopy process for manipulating multiferroic BiFeO3 nanodots smaller than 15nm to desired positions on a Nb-doped SrTiO3 substrate. For formation of the BiFeO3 nanodot array, nanocrystal movement was achieved using a +1.2V biased conducting atomic force microscopy (CAFM) followed by nanocrystal attachment to the tip. Using this method, high-density BiFeO3 nanodot arrays with a density greater than 0.5Tb/in.(2) can be achieved. Perfectly flipped ferroelectric polarization with an external electric field was observed for each BiFeO3 nanodot, whose ferroelectric properties were confirmed using piezoelectric force microscopy.