Abstract We report the realization of two-dimensional (2D) photonic crystal (PhC) holes array using synthesized processing techniques of deep UV lithography, time-multiplexed reactive ion etching (TMRIE) and focus ion beam (FIB) etching. In this study, mixed density of holes and waveguide patterns of 2D PhC structures was first formed in silicon on insulator wafers through use of a scanner. Ultra wide grooves were then defined, aligned to the deep submicron size devices. Following deep etching of more than 50 μm by TMRIE, PhC structures were then revealed for device etching. Such design of fabrication process allows realization of disparate pattern dimensions and also etching depths. Through avoidance of etch lag effect, notching of devices at interface of device silicon and buried oxide layer was avoided. At the same time, through a singular FIB etch in the final step of the process following buried oxide release for PhC structures on critical dimension structures, severe loading effects of such structures were avoided to enable a wide process window of lithography and etch.