Here's the method I use..........
I start out like Berger says, you can use the a one way valve like on one wheel says too. I use this method until all the old fluid and junk from the slave cylinder has been thoroughly flushed out of the system. You might be surprised by how much crap and air bubbles comes out this way.
The only problem with this method is that the master cylinder moves such a tiny amount of fluid that it is difficult to get all the air out this way, especially when doing the Front brake. The air bubbles in the front brake line want to keep rising to the top.
I go over to the medical supply place and buy irrigating syringes for about $1.50 each, and one of those little tulip shaped bulbs you would use to clean out your ears or a baby's nose.
Get a length of clear plastic tubing that fits over the brake bleeder at the slave cylinder, and over the tapered end of the syringe.
Pull the plunger out of the syringe, attach the tubing between the brake bleeder and the syringe. For the front brake I just tape the syringe to a fork leg, and for the rear I tape it to the rear tire. Now, using the first method push some fluid up into the syringe body, just leave the bleeder on the slave loose. Now add about 100cc's of brake fluid to the syringe.
Now, use the baby snot sucker to remove all the fluid from the master reservoir.
Put the plunger in the syringe and slowly start pushing brake fluid into the slave, tap on the brake line starting at the slave cylinder as you push the fluid in to free any bubbles that are stuck to the inside of the line, working your way up to the master cylinder reservoir. Keep an eye on the fluid level in the master reservoir, remove the fluid as it fills with the snot sucker. I repeat this process several times, until I do not see anymore air bubbles come into the master cylinder reservoir.
If you can have a friend help you do this, and you just keep the reservoir from over filling you will be amazed at how many really small air bubbles come out of the line, this after you thought you got all the air out the other way. And it takes a lot less time if someone helps you. As mentioned pump the lever a few times to push any air bubbles out at that end through intake at the master cylinder.
You will have a little bit of leakage around the bleed screw at the slave so just put some rags around it. When you are satisfied that you have got all the air out, just push in enough to fluid to top off the reservoir, tighten the bleed screw, and secure the master reservoir cap.
Remove the hose and clean up with a bit of contact cleaner like CRC lectra motive. I use this contact cleaner as it works good but does not attack the rubber or plastic like brake cleaner can.
When you get all done just pitch the syringe as the brake fluid will eventually start to attack it but is fine while you are doing the job.
Hope this helps.