This work addresses feature size effects (the lag-effect and roughness development) in chemically assisted ion beam etching (CAIBE) etching of InP-based photonic crystals. Photonic crystal fields with varying hole size and periods were etched with different etching times. The slope of the etch depth versus diameter curves (lag-curves) reveals a hole size dependence, with a critical aspect ratio higher than 25. A model for the etch rate specific to Ar/Cl2 CAIBE is proposed. We calculate the etch rate using a physico-chemical model which takes in to account the effect of Ar-ion sputtering and surface chemical reactions. In addition, it combines the aspect ratio dependence of the gas conductance of the etched holes. The origin and evolution of the bottom roughness of the etched holes is examined. The impact of the feature size dependence of the etching on the photonic crystal optical properties is then assessed by measuring the quality-factor of one-dimensional Fabry-Perot cavities using the Internal Light Source method, and discussed in terms of hole shape and depth. A systematic trend between the determined quality factor (Q) and the lag-effect is evidenced: Q decreases from about 250 to 60 when the hole depth drops from 5 μm to 2 μm.