The authors experimentally investigate the effects of atomic layer deposition (ALD) and laser-assisted oxidation on the optical modes in GaAs L3 photonic crystal air-bridge cavities, using layers of InAs quantum dots as internal light source. Four distinct optical mode peaks are observed in the photonic bandgap and they show different wavelength-redshifts (0-6.5 nm) as the photonic crystal surface is coated with an Al2O3 layer (0-5.4 nm thick). Numerical finite-difference time-domain (FDTD) simulations can well-reproduce the experimental result and give insight into the origin of the shifts of modes with different spatial profiles. By combining the ALD coating with in situ laser-assisted oxidation, we are able to both redshift and blueshift the optical modes and we attribute the blueshift to the formation of a GaAs-oxide at the expense of GaAs at the interface between GaAs and the Al2O3 layer. This result can be quantitatively reproduced by including a GaAs-oxide layer into the FDTD model. Selective etching experiments, confirm that this GaAs-oxide layer is mainly at the interface between GaAs and Al2O3 layers. (C) 2011 American Institute of Physics. [doi:10.1063/1.3559269]