Photonic crystal (PhC) structures are often fabricated on epi-wafers with a heterostructure to realize various micro- or nanophotonic devices by dry etching processes. We discuss the dry etching process for a GaAs/AlGaAs-based epi-wafer using a resist mask to fabricate a proposed PhC laser. The epi-wafer has multiple stacked layers of InAs quantum dots (QDs) with a high density of 6 × 1010 cm−2, which cause the reduction of the diameter of the etched air holes. A higher density and more stacked layers of QDs intensify the reduction effect. By enhancing the physical etching effect, the verticality of the profile of the air holes etched in the epi-wafer with a five stacked InAs QD layers is greatly improved. The results show that the improved etching conditions make it feasible to fabricate the proposed PhC laser structure.