Most people don't have the tools to propely measure a cylinder. The error induced in hack metods is often greater than the total desired clearance. I laugh when I see someone go at a cylinder with a caliper.
Thats why I say unless you have these tools or go to a shop that does don't bother. What widebear describes is the best way to do a top end but how many of us actually do that? I just do the initial idle for 10 min cycle, then several short hard runs with cooldowns. My stuff looks fine when taken down.