Ok, first to properly bleed the brakes it takes 2 people. If what you're calling the "filter" is the rubber cup inside the fluid reservoir, take that out to add fluid. If you expect fluid to go in one end, then you need to let it out the other end, that's what the bleeder valve on the caliper is for. The procedure to bleed them is:
1. Push pedal down, and get someone to crack open the bleeder (put a hose over the end or something, fluid can squirt out and you don't want to get this stuff in your eyes)
2. When pedal goes all the way down, close the bleeder
3. Push the pedal down again, crack the bleeder open, close it, and release the pedal.
4. Watch your fluid level, and don't let it get too low. If it gets too low and sucks in air you have to start all over again.
5. Repeat until no more air comes out of the bleeder valve when you crack it open.
But if you took everything apart (why the **** did you take it apart to begin with) you might have to get a vacuum bleeder to get all the air out of the system. When the entire system gets drained air can get stuck in certain parts of the system, and refuses to come out from the normal procedure.