You need to bleed the system. The basics are to put a clear hose over the slave bleeder fitting, (I like to break the bleeder loose before putting the hose on it). Remove the master cap and fill it with fluid. Have a helper depress and hold the pedal to the floor, (say, "down"), loosen the bleeder; some fluid will enter the hose; watch for bubbles. Tighten the bleeder, (not all the way, just till snug), and say "Up", your helper will let off the pedal. Repeat this process until no more bubbles appear, or the pedal is firm, then fully tighten bleeder valve and fill/cap the master.
BIG NOTE HERE!!!!
Check the fluid level in the master EVERY 3 PUMPS! you will need to fill the master to the top after 3 pumps; if you go to 4, you may suck in air and be worse off than when you started!