When I've done it, I started by sucking out as much of the fluid from the reservoir as possible, using a turkey baster. Then I refill the reservoir with fresh fluid and bleed the brakes. Be sure to keep the reservoir topped off as you go, so you don't suck air into the lines. This gets everything except the ABS pump.
If you have access to a Tech2 scanner, there's a process for bleeding that, too. But I've never done it. I guess you could go on a drive and intentionally panic-stop to activate the pump. This would mix the fluid and hopefully get most of the crud out of the pump. But to get it all, you'd have to re-bleed the whole system a second time.