The current process to create transistors in a silicon layer uses lithography, a technique to print the required circuit creating semiconductors and other parts. The methodology is very precise, currently perhaps with the mark at 22nm for the general market and with possibilities of continuing until the atom size or that's what some people say.
A usual atom has a diameter of a 0.1nm to 0.5nm, and let's remind that the nano prefix means ten to the power of minus nine. A millimeter is then one million nanometers! The silicon lithography process permits considerable development even when fifty years ago the electricity was not fully implemented in every developed country.
The silicon substrate, other times called a wafer, is normally cut from a big cylinder in several sizes. Thanks to a photoresist element, and a source of radiation —light—, it's possible to print in the silicon stone the desired pattern. This is the same principle used for instance in silk screening, to apply drawing in t-shirts, metal or almost any material that accepts common paint.