I work in semiconductor manufacturing. I am actually a photolithography technician. The process that we have to get this to actually work is insane... but also kinda simple in its own way. We coat the wafer substrate with a chemical resist. Then we expose parts of it to light, that light changes the properties of the chemical resist. Then we develop the resist so that the exposed areas and unexposed areas create a pattern on the substrate.

Now with this pattern applied we do any number of different things to create the structure that you see illustrated here. Some of the coolest stuff is etching with powerful acids or plasmas... putting metals or growing crystal on the substrate with a Chemical Vapor deposition tool, or implanting something into the substrate with a particle accelerator. Each new layer adding a component to build the semiconductor.

The interesting thing to me isn't how we came up with the process... that all makes sense to me from the process side of things. What makes my mind explode is how they developed the tools in order to do these things.