Atomic force microscope (AFM) is a detection device with nano-level precision, which can be utilized to fabricate nanostructures. It has been one of the effective approaches to machine nanostructures and widely used in fields of mechanical engineering, physics, chemistry and biomedicine. Traditional micro/nanofabrication methods were introduced briefly at first. Subsequently, the nanofabrication method based on AFM was described in details and the corresponding advantages were analyzed. The applications of the nanostructures that machined using AFM such as nanochannel and nanodot in fields of nanofluidic and Raman detection were presented. The prospects for future research were put forward at the end of this paper. This review demonstrates the application potential of AFM nanofabrication and provides a necessary nanomachining approach for the research in related fields.