We succeeded in controlling the apparent size of a colloidal PbS quantum dot (QD) in the range of 20 to 140nm by coating with silica and trapping the coated QDs in a nanohole prepared by scanning probe microscope lithography. Photoluminescence intensity was improved by controlling the process of adding the silica source material of tetraethoxysilane for the coating. Nanoholes of different sizes were formed on a single substrate by scanning probe oxidation with the combination of SF6 dry etching and KOH wet etching. QDs having an arbitrary energy structure can be arranged at an arbitrary position on the semiconductor substrate using this technique, which will aid in the fabrication of future nanosize solid devices such as quantum information circuits.