We study the modifications on the three-dimensional transport properties of Si-doped AlGaAs layers exposed to CH4/H-2 reactive ion etching (RIE) by using the temperature dependence of Hall measurements. The persistent photoconductivity (PPC) effect is observed for the samples illuminated at low temperature (4.2 K). A strong capture region is observed between 100 and 160 K. Different annealing temperatures (between 300 and 450 degrees C) are used to study the effect of the passivation of Si donors and DX centers on the PPC. For annealing temperatures lower than 350 degrees C a new capture region is identified and attributed to the DX3 center. Also, the resistivity and mobility are modified by RIE exposure. The transport characteristics are recovered after thermal annealing at temperatures higher than 400 degrees C.