Provided is a method of fabricating a probe for a scanning probe microscope (SPM) having a field effect transistor (FET) channel structure utilizing a self-aligned fabrication. The provided method includes a first step of forming a first-shaped mask layer on a substrate and forming a source region and a drain region in regions of the substrate except for the mask layer; a second step of patterning a first-shaped photoresist in a perpendicular direction to the mask layer and performing an etching process to form a second-shaped mask layer; and a third step of etching the regions of the substrate except for the mask layer to form a probe. The provided method aligns the center of a tip with the center of a channel existing between the source region and the drain region to realize a tip having a size of tens of nanometers. Thus, a nano-device can be easily manufactured using the probe having the tip.