I use the G5 Arrow Squaring Device. Other folks use some homemade devices. Basically, what you do is take something to grind/sand the ends so that they are square to the shaft length. The G5 ASD has a setup that, when you lay the arrow on the V notches, places the shaft exactly perpindicular to the grinding/sanding surface. If you were to make a home made device you would just need to make sure that the shaft was perfectly square to whatever grinding/sanding device you would use.

The ASD works with carbon or aluminum arrows.

http://www.g5outdoors.com/#sec_asdtool