A method for protecting an ion-implanted substrate during the annealing process by covering the ion-implanted layer with a suitable encapsulant. A thin layer of ions are implanted into a GaAs substrate. A protective layer of germanium, amorphous GaAs, doped GaAs, or GaAlAs is applied over the implanted layer and on the periphery of the ion-implanted GaAs substrate. The composite is annealed at a temperature which is adequate for the lattice to recover from the ion-implantation-induced damage. The protective layer is removed subsequent to the anneal step, without any damage to the ion-implanted layer.