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Provided is a SOI wafer manufacturing method in which an ion injection layer is formed by injecting one or more type of gas ions selected from hydrogen and rare gases from the surface of a bond wafer made of a semiconductor single crystal substrate, and, after the base wafer surface and the ion-injected surface of the bond wafer are bonding with an oxidation layer interposed therebetween, separation heat treatment is performed in a heat treatment furnace and the bond wafer is separated at the ion injection layer, manufacturing a SOI wafer. After the separation heat treatment, once the temperature has been reduced to 250°C or less at a cooling rate of slower than 3.0°C/min, the separated SOI wafer and bond wafer are removed from the heat treatment furnace. By this means, a method of manufacturing SOI wafers is provided which avoids scratches and irregularities in SOI film thickness.