Are you using vacuum to pull the fluid from the calipers? If so, the small bubbles you see from air drawing in around the bleeder nipple threads is normal and not a concern.
If you have air in the calipers, it comes out fairly easily if you follow the suggested bleeding sequence AND assuming that your calipers were assembled properly. Search this board for discussions on that topic.
If you have air in the master cylinder because it is new or rebuilt, you probably need to 'bench bleed' it. Buy a short length of metal brake line, cut it in half, bend it into two "J" shapes, screw the ends into the outlets of your master cylinder such that the fluid is returned to the reservoir, and pump ~aggressively until there is no more air, then install the master cylinder.
If you have air in the system between the master cylinder and the calipers, there are a couple of spots that are really hard to clear of air. A pressure bleeder is the only reliable method. You can find various designs of pressure bleeders on line, at prices from $25 and up.
P.S. If your master cylinder is rusty or cruddy inside, pressing the pedal to the floor while bleeding pushes the rubber seals into an area of the master cylinder bore where they don't normally go. The rust and crud can trash them, rendering your master cylinder useless. Oh well, it needed replacing anyway.
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