Thin films of Al, AlN, Si, and Si3N4 deposited on GaAs substrates were irradiated with silicon ions. The amount of interfacial mixing was found to depend both on the composition of the thin film and on the ion dose. The greatest amount of mixing, as measured by Rutherford backscattering spectrometry and Auger depth profiling, occurred in the Al/GaAs system. Mixing in the Si/GaAs system showed a sublinear dose dependence as well as a deep diffusion of silicon into the substrate. Interfacial phase formation between the aluminum and silicon layers and the GaAs substrate was observed using Auger line shape analysis and low-energy electron loss spectroscopy. Small or negligible mixing was found in the AlN/GaAs and the Si3N 4/GaAs systems, presumably due to strong nitrogen bonding in these layers. The data suggest that an optimal cap for through-cap implantation and annealing is a two-layer structure consisting of a thin Si3N 4 layer below a thick AlN layer.