Radiation damage due to electron beam annealing has been investigated in MOS devices underlying an electron beam annealed Silicon-on-Insulator structure. A high degree of residual damage (surface state and positive charge) is found to exist in MOS devices. The damage can be easily annealed out by low temperature (500–550°C) furnace annealing, when underlying MOS devices exist outside the electron beam range. However, high temperature furnace annealing at about 1000°C is necessary to eliminate the damage, when the electron beam penetrate through the gate oxides in MOS devices. Use of a low energy electron beam is recommended, based on these results, for the Silicon-on-Insulator formation for three-dimensional ICs.