Layer-by-layer removal of Si atoms from the Si(111)-7×7 surface was executed at room temperature by making a point contact of a biased W tip of scanning tunneling microscope (STM) to the sample surface. The adatom layer and the three layers were controllably removed by tuning the sample bias voltage. In the created holes, clear atomic images were obtained. The current between the STM tip and substrate exhibited characteristic structures during the tip excursion, which are closely related with the atom removal process and the nature of the Si nanoscale wire, respectively.