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Nanoscale surface modification of a fractured Nb-doped SrTiO3 surface is demonstrated in a controlled way by scanning tunneling microscopy. By applying positive voltage pulses, holes can be created and the width and depth of the hole can be controlled by selecting the appropriate bias and pulse duration. The process shows a threshold condition for creation of the holes and change in the local electronic density of state consistent with exposure of the underlying TiO2 layer by removal of SrO. By applying negative bias, the hole can be partially refilled from the transfer of adsorbates on the tip. [ABSTRACT FROM AUTHOR]