There are some systems that do direct write, but they are intrinsicly serial, as opposed to the massively parallel nature of scanners, which have a huge throughput advantage. Direct write only serves markets where small quantities are required, and price is no object (military). If NSA needs a couple of hundred ultra-specialized crypto chips, they can use a direct writing system. Micromirror (TI) chips allow direct write throughput to go up, but still fall far short of scanners or steppers on the throughput front.
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