Overview
Piston to valve clearance deals with the space between the valve and the piston during a critical point in the cam timing knows as the "overlap period". At no other point in the four stroke cycle does the valve get closer to the piston. Thus it is imperative that enough clearance exist in order to avoid a collision between the piston and the valve.

The overlap period occurs near the end of the exhaust stroke and at the beginning of the intake stroke, when both valves are open for a short

During Overlap both valves are open as the piston rises.
period of time. Overlap is a critical period in the cam cycle, as the movement of exhaust gases out of the combustion chamber "draws" in a fresh charge through the intake valve.

Many people have even erroneously measured clearance at the point of maximum valve lift, thinking that is the most likely point at which interference would occur. However when a valve reaches its maximum lift, the piston is actually the furthest away since this occurs during the intake stroke, when the piston is moving down the cylinder bore.

 Minimum clearances between the valve and piston should be 0.080" on the intake valve, and 0.100" on the exhaust valve. If you run aluminum rods, the clearances should be even greater. In this article we'll show you the two methods most commonly used to measure piston to valve clearance.
Clay Method

There are a couple ways to check for clearance. One way is to place a 1/4" thick strip of clay on the piston, and turn the engine over through one full cycle (two rotations past TDC) allowing the valves to make an impression in the clay.

The downside to clay is that the heads must come off to do the check. Clay is also cumbersome, it tends to stick to the piston, and requires a lot of practice to get reliable measurements.
The clay is then carefully peeled off the piston, cut in various locations, and the thickness is measured to determine how much clearance exists. This method works well in that it gives you a three dimensional view of not only how much clearance there is, but also where the interference is occurring. This helps determine if the problem is too shallow of a valve pocket in the piston, or if the pocket is not wide enough for the valve head.
 
Spring Method

This involves using a light weight valve spring and a feeler gauge. The procedure is to replace the intake and exhaust valve springs for one cylinder with light tension "checking" springs. They can be bought at any hardware store for under a dollar. They must fit squarely between the seat and retainer and be just stiff enough to hold the valve closed.

Adjust the rockers to zero lash, irregardless of whether it is a hydraulic or a solid lifter. It is extremely important if you are using a hydraulic lifter, to AVOID preloading the lifter. Instead you want to remove all the slack in the pushrod, without forcing the plunger in the lifter downward. Be sure to make the lash adjustments when the cam lobes for that cylinder are on the base circle. (Piston is at Top Dead Center of the compression stroke.) A quick way to set the lash is to adjust the intake rocker when the exhaust valve just starts to open. Then adjust the exhaust rocker when the intake valve is just beginning to close (coming back up after full lift.)

The benefit to this approach is you don't have to take the heads off, but you do need to remove the valve springs with some sort of spring removal tool.
With the test cylinder ready, set your feeler gauges to 0.100". Starting with the piston at top dead center of the compression stroke, rotate the crank one full cycle in direction of normal rotation.

As the piston travels back up the bore the exhaust valve opens and the exhaust stroke begins. Keep an eye on the valve train, and you will notice the exhaust valve spring slowly compress as the valve fully opens. As you approach TDC you will notice the intake will begin to open before the exhaust valve has fully closed. This period, roughly 10-15 degrees before and after TDC is the overlap period. Both valves are slightly open and piston is near the top.

It is precisely during this overlap period where you'll want to use the feeler gauge to measure the distance between the valve stem and the rocker arm tip or roller. The piston is so close to the valves at this point that you can push down on the checking spring and feel the valve contact the piston. It is this distance which is critical, and needs to be a minimum of 0.080" on the intake side, and 0.100" on the exhaust. It may take several cycles to get the hang of where the overlap period is and how to take the measurements.

Conclusion
You will notice that the overlap period does not last very long, and in fact it is very easy to miss. In terms of degrees of crankshaft rotation, the total overlap period may be as little as 40 degrees for a mild cam, in other words 20 degrees before and 20 degrees after TDC. At some point within this range the piston and valve will be the closest. Therefore it is imperative to check the clearance at least every two degrees during the overlap period.

Take a few measurements, then rotate the crank a few times and check again until you get the same number each time you measure.
A helpful trick is to push down on the retainer with your thumb so that the valve a contacts the piston. Use your index finger to keep the rocker arm taught against the pushrod. As you rotate the crank the valve will "ride" the piston, and you will be able to see the space between the valve stem and rocker tip get smaller and smaller during the overlap period. Use your feeler gauge to measure the point where the gap is the smallest.

If you determine that you have at least .080" on the intake and .100" on the exhaust side then you have sufficient clearance to run that cam.

In the event you don't have enough clearance, there are several options. The easiest option is to not use that cam. Most people don't want to hear that, especially since they've already paid for the cam. This leaves a couple options in order to achieve the necessary clearance.

If your clearances are relatively close, within 0.010", you can attempt to retard or advance the camshaft. Retarding the cam effectively opens the exhaust valve earlier and the intake valve later. This translates to a few thousandths of an inch more clearance on the intake side, and roughly the same amount less on the exhaust side. In the case where your intake valve clearance was running close, and your exhaust side had plenty to spare, you could retard the camshaft 2 to 6 degrees and gain some clearance. Conversely, advancing a cam will bring the intake closer and the exhaust slightly further from the piston during overlap.

Realize, however, that when you advance or retard a cam you change the performance characteristics and power-band that was designed by the manufacturer.

The other option is to replace the pistons with aftermarket types which accommodate larger valves. Replacing pistons means a significant amount of work and money in tearing down and rebuilding the motor. However in the end an aftermarket piston with a deep valve pocket will ensure proper clearance.

The final solution is to notch the existing pistons. The following steps detail how to accomplish this.


Gaining Clearance

Put a dab of white latex paint on the valve face, and then with the head on the block and the piston at TDC, force the valve down until it contacts the piston.
This results in the paint transferring on to the piston in precisely the location which needs clearancing. In this case, to the right of each intake valve relief.
 

With all the pistons marked, put a grinding stone on the Dremel® tool or die-grinder and carefully extend the valve relief's. Stop often to install the head and to remeasure the clearance. Try not to over do it, as removing weight results in upsetting the balance of the motor, and also weakens the piston. Be sure to take all the necessary precautions to keep the grindings out of the motor. We covered up all the adjacent cylinders and used a shop vac to suck the grindings up before we moved on.
The "professional" way to do this is to buy a piston notching tool, such as the Isky Cams product shown here. The tool is simply a valve head with "teeth" on the face. This head attaches to an arbor, and is then installed in place of the valve in the cylinder head. A drill is attached to the arbor and used to turn the tool, and as a result the teeth grind the piston exactly where the valve would contact. The tool comes in various valve and guide diameters to work with basically any popular engine and head combo.