The neck is the area of the guitar which the strings will rest above.

Measure out about 3-4" at the end of the neck to cut out a head stock as pictured.

I saved the head stock scrap to test wood finishes on later, but that is optional.

Place the neck inside the box, then mark off where the edges of the lid touch the neck.

Measure in 1/4" from those edges, and cut 1/4" relief cuts about 1/8" apart from one side of where the neck touches the lid to the other. I marked off this section with dark graphite so I would know where to cut to.

Once you have these cuts, tap out a couple of the relief cuts with a hammer and flat head screwdriver. You do not need to hit hard, just enough to break the pieces.

Once you have about 1" tapped out, you can cut out the rest with a table saw.

This section does not need to look pretty, as it will be inside the box and out of view.

Drill three 1/16" evenly spaced holes on the opposite end of the head stock. This is where your strings will pass through.