There have been tremendous interests about the fabrication of metallic nanopore due to the ultrafast genome sequencing biosensor capability. In this report, the fabrication of the nanopore on the Au coated SiO2 pyramid has been examined using various high energy electron beam irradiation and focused ion beam (FIB) milling techniques. The microfabricated Au nano-apertures on pyramid were irradiated with various high energy electron beam and FIB techniques. The formation of the nanopore dependent on the probe current was also examined using electron probe micro-analysis (EPMA). The nanopore on the Au coated SiO2 pyramid is found to be an Au Si mixture. The Au nanopore on the crater type hole was also fabricated using FIB Ga ion beam scanning. The shrinking rate was found to be the fastest compared with those fabricated with the other electron beam techniques. Crown Copyright (C) 2014 Published by Elsevier B.V. All rights reserved.