A periodic structure of bonded GaAs wafers has been proposed for quasi-phase-matched second-harmonic generation. However, current bonding processes used to fabricate these structures often lead to unacceptably high optical losses. When commercial semi-insulating GaAs wafers were bonded at 850°C, increases in the free-hole concentration (thermal conversion) were found to be a major cause of excess optical loss. This conversion depended on both the GaAs source and the materials composing the sample holder. We found that quartz and sapphire could not be used in contact with GaAs wafers because they stuck during the bonding process. On the other hand As-charged graphite holders did not stick and worked well under our bonding conditions.