That video the BigBob posted from Delboy's Garage is the method I use to realign my forks after doing a fork service. If you want the step by step, these are the directions that I made to keep in my service manual:
HOW TO ALIGN THE FORKS
1) Loosen the large cap nut on the top of the upper fork clamp. It's that big nut in the center of the clamp, right below the ignition. This allows the upper clamp to move. DO NOT loosen the pinch bolts on the upper clamp that hold the fork tubes.
2) Loosen the four pinch bolts on the lower fork clamp.
3) Loosen the front axle.
4) Loosen the fender.
5) The bike has to be perpendicular to the ground for this, but don't use the centerstand. The centerstand wont allow you to put enough weight onto the front of the bike. Either secure the rear wheel in a paddock stand, or have a helper hold the bike upright.
6) Get on the bike and bounce the front end a half dozen times.
7) Get off the bike while the helper holds it vertical. Don’t put the bike on the center stand or sidestand yet.
8) While the helper holds the bike, snug down the cap nut on top of the upper fork clamp. Hold the forks so the clamp doesn’t move while you tighten it. You don’t have to tighten it all the way at this point, just get it snug.
9) Snug down the pinch bolts on the lower fork clamp. Work side to side to keep it even.
10) Snug down the bolts on the fender.
11) Snug down the axle.
12) Now torque the cap nut on the upper fork clamp.
13) Now torque the pinch bolts on the lower fork clamp.
14) Now torque the bolts on the fender
15) Now torque the axle.
16) Now torque the axle pinch bolts.
17) Done.
I attached a PDF copy of the instructions I use, if you want a copy for yourself.