Local modification of H-terminated n-Si(100) surface in an aqueous hydrofluoric acid (HF) solution was carried out under anodic and cathodic potential polarization with an in situ scanning tunneling microscope (STM). Two different modifications in the HF solution were obtained. At cathodic polarized potential, H-terminated silicon surface is attacked by HF at the defects of silicon surface under an electric field between the tip and silicon surface. However, at anodic polarized potential (by applying positive potential pulses), the nanostructures produced are probably due to the formation of silicon oxide. The apparent depth of the nanostructures, as observed with the STM, decreases with time because of the dissolution of silicon oxide in the solution. Effects of the tunneling current, the potential of silicon surface, and pulse amplitude show that the formation of silicon oxide is dependent on the electric field and local electrochemical oxidation of silicon surface at anodic potential.