We demonstrate the preparation and exploitation of multilayer metal oxide hard masks for lithography and 3D nanofabrication. Atomic layer deposition (ALD) and focused ion beam (FIB) technologies are applied for mask deposition and mask patterning, respectively. A combination of ALD and FIB was used and a patterning procedure was developed to avoid the ion beam defects commonly met when using FIB alone for microfabrication. ALD grown Al2O3/Ta2O5/Al2O3 thin film stacks were FIB milled with 30 keV gallium ions and chemically etched in 5% tetramethylammonium hydroxide at 50 °C. With metal evaporation, multilayers consisting of amorphous oxides Al2O3 and Ta2O5 can be tailored for use in 2D lift-off processing, in preparation of embedded sub-100 nm metal lines and for multilevel electrical contacts. Good pattern transfer was achieved by lift-off process from the 2D hard mask for micro- and nano-scaled fabrication. As a demonstration of the applicability of this method to 3D structures, self-supporting 3D Ta2O5 masks were made from a film stack on gold particles. Finally, thin film resistors were fabricated by utilizing controlled stiction of suspended Ta2O5 structures.