How come we don’t make chips with really small 3d printers?
The closest thing there is is e-beam lithography. It isn't really practical.
AFAIK you can't really print crystalline silicon so they have to start with a wafer and dope/etch into it to form transistors.
Sibling has a good comment about silicon. Another reason you're printing something like 100B transistors. So that's at least 100B raster steps. It would just take too long.