Nanoscale amorphous marks have been produced in crystalline Ge2Sb2Te5 films using an atomic-force microscope (AFM) and a scanning-tunneling microscope (STM) through electrical phase changes. Voltage pulses with duration of 5–100 ns applied by metal probes of the AFM and the STM can produce, respectively, high-resistance regions and deformations, the smallest sizes being ~10 and ~100 nm in diameter. Raman-scattering spectra demonstrate that these marks are amorphous. The AFM mark can be erased by applying longer pulses. Formation processes of the marks are considered from electrothermal and thermodynamic aspects.