A novel aluminum oxide (Al2O3) hard mask fabrication process with nanoscale resolution is introduced. The Al2O3 mask can be used for various purposes, but in this work it was utilized for silicon patterning using cryogenic deep reactive ion etching (DRIE). The patterning of Al2O3 is a two-step process utilizing focused ion beam (FIB) irradiation combined with wet chemical etching. Gallium (Ga+) FIB maskless patterning confers wet etch selectivity between the irradiated region and the non-irradiated one on the Al2O3 layer, and mask patterns can easily be revealed by wet etching. This method is a modification of Ga+ FIB mask patterning for the silicon etch stop, which eliminates the detrimental lattice damage and doping of the silicon substrate in critical devices. The shallow surface gallium FIB irradiated Al2O3 mask protects the underlying silicon from Ga+ ions. The performance of the masking capacity was tested by drawing pairs consisting of a line and an empty space with varying width. The best result was seven such pairs for 1 μm. The smallest half pitch was 59 nm. This method is capable of arbitrary pattern generation. The fabrication of a freestanding single-ended tuning fork resonator utilizing the introduced masking method is demonstrated.