If there are billions of transistors in a CPU, there is no chance that somebody designed every single one of them manually. Is their layout calculated or something?
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The main idea use is “design hierarchy”. You would design a transistor, than use that design to build a set of logic gates to match of set of requirements that you need. Then you would use those designs to built larger and larger devices until you have built the entire device. There are specific CAD tools use to do layout with (such as Cadence) and human readable languages for doing the top level design (Verilog and VHDL), so there is some automation in the process. However, you would also use those tools to test your design to see if it performs as required, then adjust the parts that are not performing as required manually until you get a design that works.
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