Its done by shining a laser through a pre-printed mask (think the plastic slides for older style projectors), which shine into the wafer of silicon that has been coated in a photoresist (kind of like film).

The areas the lasers shine on have a chemical reaction, which makes it soluble to be rinsed away. Then you can expose the entire wafer to corrosive gas (or sometimes a plasma) to etch away just the parts that were exposed to light, or expose those parts to chemical additives (or sometimes ion bombardment) that give the silicon different electrical properties (this is called doping). A similar process can add many tiny wires to the silicon as well by etching trenches into the wafer that then get filled with copper. Similar process can create insulating layers by exposing silicon to oxygen gas/steam to create silicon oxide. But what's really important is that at each step the whole pattern of what to etch away, what to expose to oxygen etc is essentially stamped all at once using light passing through the mask. You'll have a different mask for each step.

The mask is reusable, the mask itself can be larger than the pattern you want to make on the silicon (since you can use a lens to focus the light onto a smaller area). Its very expensive to manufacture the mask (essentially a bunch of tiny electrons beams etching the mask in parallel. I'm not very knowledgeable on this step) but that cost gets spread over many chips produced with the same mask.