The effect of surface passivation in BCl3/N-2 inductively coupled plasma reactive-ion etching of GaAs-based photonic crystals (PhCs) was investigated. It is shown that sidewall passivation is crucial for achieving cylindrical, vertical PhC holes, where the exact shape of the hole is controlled via the N-2 content in the plasma composition. The achieved quality of PhC membrane cavities was established by optical characterization of such cavities incorporating site-controlled quantum wires as integrated light source. (C) 2009 American Vacuum Society. [DOI:10.1116/1.3205004]