Experimental results and techniques developed for time multiplexed deep reactive ion etching of nano-photonic crystals are presented. Specifically, the high aspect ratio pillar type two-dimensional photonic crystal (PhC) structure on silicon is fabricated and studied for its high potential in application to lightwave circuits and also for discussion of the many unique challenges involved in its fabrication process as opposed to standard larger scale devices. In the experiments, patterns of nano-dots were first obtained using deep UV lithography and transferred to a silicon oxide hardmask prior to DRIE processing. The iteration of DRIE experiments with varying process parameters then allowed for a characterization of the varying impact of each etching parameter such as coil/ platen/ etch power, multiplexing cycling gas flows and timing patterns etc. After much optimization of sidewall etch angle and also reduction of the scalloping effect, the latest result obtained for such nano-pillar type PhC designed for application in communication is derived to have a high AR of 33.