The surface of the head that mates to the block must be extremely flat, otherwise the gases in the combustion chamber will leak between the head and the block. No hills or dips may be present. To put this into perspective, the specifications for a diesel engine head were defined by the non-profit trade group Aero Engine Rebuilders Association. The mating surface cannot have a waver of more than 5 thousandths of an inch. A sheet of common writing paper is about 3 thousandths of an inch thick. In other words, the entire mating surface of the head cannot have a hill or valley thicker than a sheet of paper.
The valve stems to the valve stem bores have precise specifications, as well. If the stem is too tight in the bore, the expansion caused by heat will make it bind. If the valve stem is too loose, it will allow oil to leak into the combustion chamber. This clearance is typically about 2 thousandths of an inch for the intakes, and about 3 thousandths of an inch for the exhaust valves. In other words, the bore has to be about 2 to 3 thousandths of an inch bigger than the valve stems. Different manufacturers set this specification for their engines. However, over time, a valve stem may get "sloppy" inside the bore because of wear.
Engineers draw up specifications for the heads, and manufacturing makes the heads. Problems occur between the drawing board and the final product. Researchers at the University of Michigan define what these problems are in a case study of cylinder heads. Making a cylinder head is done by multi-machining processes, or MMP. One machine drills the valve stem bores, and another machine mills the mating surface flat. One machine may be "a little off" from the blueprints, but not enough to cause worry. The next machine may be a little off, too. The next machine is also a little off. The problem is that all the "little offs" add up to make one big off, and the end result is the head is out of tolerance. The cure is all the machines have to be as close as possible to the design specifications on the blueprints. For example, if the prints call for a hole to be bored at .500 of an inch, the boring machine cannot bore the hole at .503 of an inch.