The entire ingot can be doped by including certain impurities when making it (or by exposing it to a powerful neutron flux from a nuclear reactor). But the tiny individual doping operations are done photographically. A compound is placed on the wafer, and a mask is used to expose certain areas of it to light to harden it. The parts that did not get hardened can be washed away with chemicals, leaving only specific areas of silicon exposed to be doped. Then, the hardened areas are removed with other chemicals. Rinse and repeat.
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