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when you diffuse drain and diffusion areas,they automatically aligns beneath the polysilicon(as polysilicon acts as a mask)..This is called self aligned structure..
usually it refers to the famous CMOS diffusion implanting process, first the poly gate and gate oxide id build up , then use ion implanting to hit wafer surface, it will be blocked by the poly gate, but the exposed drain and source will be penetrated by the implanting ions and gradually, drain and source is formed to make a complete transistor, that is so-called self-align structure.
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