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We present a transmission model for estimating the effect of the atomic-force microscopy tapping tip height on a photonic crystal microcavity (MC). This model uses a fit of the measured tip-height-dependent transmission above a Â¿hot spotÂ¿ in the MC. The predicted transmission versus average tapping height is in good agreement with the values obtained from tapping mode experiments. Furthermore, we show that for the existing, nonoptimized structure, the transmission coefficient can be tuned between 0.32 and 0.8 by varying the average tapping height from 26 to 265 nm. A transmission larger than that of the undisturbed cavity at resonance was observed at specific tip locations just outside the cavity-terminating holes.