We present nanostructure fabrication techniques using field evaporation and local heating in scanning probe microscopes, especially the scanning tunneling microscope (STM), atomic force microscope (AFM), and the scanning near-field optical microscope (SNOM). The detachment of sulfur atoms from the surface of cleaved MoS2 and atomic scale fabrication were demonstrated with a field evaporation in STM. Field evaporation in AFM forms nanometer-sized gold dots on a SiO2/Si substrate. Local heating with SNOM changes a phase of the GeSbTe recording film from amorphous to crystalline, and forms high reflectivity domains 60 nm in diameter. Moreover, we discuss these applications to a semiconductor process and data storage.