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If you want to lower the action on an acoustic guitar by filing the notches on the nut, you'll need a set of nut files that corresponds to the gauge of string you're using. Since each string is a different thickness, you'll need a set of six nut files – one for each string.  If you don't have a set of nut files, you can typically find them at a luthier supply shop, as well as at many music stores. You'll also need a feeler gauge so you can measure the action at each fret and file accordingly. If it isn't already, you need to make sure all six strings of your guitar are in tune before you start measuring the action at the nut and making adjustments. Place your feeler gauges right on top of the first fret so you can determine how much the nut needs to be filed down to lower the action.  Use a ruler to measure first. It should be 0.3 inches or about 7.5 millimeters from the string to the first fret. If it's greater than that, keep checking the distance using larger feeler gauges until the string moves because the gauge is too big to fit. The distance between the string and the fret is the thickness of the largest feeler gauge that doesn't cause the string to move. Repeat this with each of the six strings. Carefully loosen the string, only enough to pop it out of the nut without damaging the nut. Loosen it just enough that you can easily pop it out and thread it along the side of the nut. Find the nut file that corresponds to the sixth string and get a piece of plastic or masonite to protect the headstock so you don't file the headstock while filing the nut.  Place your nut file in the notch and file carefully, going in the direction of the headstock at the same angle. Only file a small amount at a time, as you cannot replace material once you've filed it down and you don't want to file it down too much. When you think you're done, replace the string, tune it, and measure it again to see if you need to refile or if you've corrected your problem. Once you've got the notch for your sixth string filed correctly, you'll want to repeat the process with each of the other five strings to lower the action on your guitar at the nut.

Summary:
Gather basic tools. Tune your guitar. Use a feeler gauge to measure the action at the first fret. Loosen the sixth string. File the nut with the appropriate nut file. Repeat with each of the other strings.