Fabrication of a new class of quantum structure which has a buried nickel (Ni) dot in a split-gate quantum wire using a scanning tunneling microscope (STM) is described. In order to fabricate small structures at the desired wire surface position, we employ a combined STM/scanning electron microscope (SEM) system in high vacuum. The fabrication methods are those based on simple electrical evaporation with a tungsten (W) tip. On the free surface far from the split-gate electrodes, the structure produced after applying a single voltage pulse is a small mesa (150 nm diameter, 20 nm high). However near the gates, large holes (150 nm diameter at half-depth, 85 nm deep) are created. Such large holes act as the pinpoint antidot for the two-dimensional electron gas (2DEG) lying at a depth of 60 nm from the wafer surface. As a metallic material, we adopted a Ni. For burying Ni into the hole, we moved the Ni-coated W tip to the hole bottom by observing the SEM image and created a Ni dot in the hole by applying a single voltage pulse.