The effect of rapid thermal annealing (RTA) on the shapes of GaAs/AlGaAs quantum wells (QWs) has been investigated by monitoring exciton energies using low-temperature photoluminescence and photoluminescence excitation spectroscopies. After RTA, large changes in exciton energies were observed only in regions of the samples in which excess surface vacancies were generated, either by capping with a thin layer of SiO2 or by low-energy ion implantation. These changes were interpreted as resulting from modifications of the shapes of the as-grown QWs from abrupt or square to gradual (rounded) due to enhanced interdiffusion of well/barrier atoms. For single QWs there was an increase in exciton energy whose magnitude depended on the width of the well, its distance from the surface of the wafer, the annealing temperature and the total number of surface vacancies available. From studies of coupled QWs, there was clear evidence of asymmetry in the heterostructure after RTA. Although both techniques of vacancy generation yield substantial QW shape modifications, the ion implanation technique has the advantages of being highly reproducible and of being compatible with any material system.