An nonvolatile memory device with self-aligned nano structure on SOI have been proposed and fabricated using E-Beam lithography and Reactive Ion Etching. The total number of masks are 6 layers, among which 2 are patterned by direct-write E-Beam lithography. Floating gate size of 0.25㎛×0.25㎛ has been achieved by the lithography limitations, successful EEPROM operation has been obtained with the threshold voltage shift $ΔV_T$ of ~0.9V.