By clearing the lines do you mean draining, or bleeding? I thought you said you drained the lines already, or did you mean the resevoir?
This is how my book says to do it, Clymer, i have a 91 zx7, if any of this is incorrect, please forgive me, but it works for me every time, and the book says this covers through 1998.
If you haven't drained all the fluid out, I wouldn't. I would start filling the resevoir up with new fluid, same type of course, and then bleed like you normally would. If you do this, be sure to bleed a little extra after no more bubbles are present, to remove any "mixed" fluids. If you have drained it all, just begin filling, and bleed as follows:
I am assuming you are using a brake line bleeder:
1. Attach the bleeder hose to the bleed valve on the clutch slave cylinder. This hose should run to the bleeder resevoir(or some kind of "catch can"). Another hose will run from the bleeder resevoir to the pump.
2. Fill the resevoir(the book says to replace cap lightly in between fillings to keep dirt from getting in it), and dont let the resevoir get empty again, be sure to keep it about a 1/4 inch above the bottom of the resevoir, or you will have to bleed that air out.
3. Open the bleed valve about 1/2 turn.
4. Pump the brake bleeder. Keep an eye on the resevoir, keep it filled. Continue to pump until no air bubbles emerge from the bleed valve.
5. Close the bleed valve. (Depending on your bleeder, be sure the resevoir on the bleeder doesn't fill up, you should empty it every so often depending on the size. If the brake bleeder resevoir fills, it will pull the fluid into the pump, which you want to avoid)
If you are not using a brake bleeder, instead using hose and a jar, you have to pump the clutch lever to bleed, but it is a little different, I will explain if you need me to.