Various nanostructures with high-aspect-ratio formed in a low-resistivity silicon wafer by the nano-processing using a carbon nanotube (CNT) probe of a scanning tunneling microscope (STM) have been investigated. The multi-wall CNT probes were obtained with our original pulling-method from CNT dispersion liquid. Nanostructures of point configurations (pit and mound) and line configurations were obtained at the constant tunneling current of 0.1 nA by controlling the bias voltages up to 10 V, processing times up to 300 s and scanning speeds of probe up to 480 nm/s for a line configuration. The aspect-ratio of the pit configuration fabricated at the bias voltage of 3 V increased about 6 times in proportion to the increase in processing time. Remarkable influence of the bias voltage on the configurations indicated that there exists a threshold bias voltage for the transition from the pit configuration to the mound one between 3 V and 5 V, and the aspect ratio of all nanostructures fabricated by the CNT probe were larger than those by a conventional tungsten probe. Finally, cross-sectional TEM observations were also applied to clarify the difference in the formation mechanisms between the pit configuration and the mound configuration. The TEM image of the pit configuration showed neither dislocations nor remarkable strains existed, but in the case of the mound shape TEM analysis indicated the existence of single crystalline silicon region solidified with atomic defects under the mound configuration. Therefore the drastic change of the configurations was attributed to the changes of the atomic-scale microstructures by applying the bias voltages.