A novel technique of Si atom removal by approaching biased scanning tunneling microscopy tip to the surface to the point contact region followed by retraction to the tunneling region was applied to Si(lll)-7X7 surface to reveal (i) the atomic structures on the newly exposed surfaces, (ii) tip-substrate current variation in relation with the Si atom removal. When the adatoms were removed, the second layer of the diameter-adatom-stacking fault model structure appeared without reconstruction except the relaxation of dimer rows. When a higher biased tip (>2 V) was contacted, the top three layers were removed. Clear metastable structures such as c(2X4) and root 3X root 3 are observed in the holes, and the shape of these structures was easily changed with the expansion of the size of the hole. A staircase shape current drop was observed in the tip retraction process when the adatoms were removed. This is considerably related to the decrease of the number of Si atoms in the tip-substrate junction with atom-by-atom manner, which shows a clear contrast to the nanowire formation in the metal surface indentation. The last drop of the current to return to the tunneling region might correspond to a junction with a single atom between tip and substrate, which corresponds to 4X10(5) Ohm. A part of the Si atoms in the junction remains on the tip which resulted in the removal of Si adatoms, which occurs with certain probability.