Air can be trapped in the master cylinder and if that is the case, no amount of bleeding the brakes at the calipers will release that air. For this reason, installation of a new master cylinder should always include bench-bleeding the master cylinder before installing it.
If the master is already installed and you suspect it has air trapped in it, I guess you could disconnect the lines and rig the master up for a bench bleed the same way you would with it out of the car, then just press the pedal a million times just like you would depress the piston with a long screwdriver if you had the master in a vice. The disadvantage there is that you are sitting in the car, so you can't watch the progress of the air bubbles through the lines - and if you haven't bench bled a master cylinder before that might not make sense, but air does not travel out of the master quickly like you're accustomed to with bleeding at the calipers. It requires a LOT of repetitions, the air will travel a quarter of an inch each time, and each time you think you've been doing it for long enough, another little bubble will appear that was trapped somewhere up inside there.
If you've got all the lines disconnected, you're just two 12mm nuts away from having the master cylinder out of the car, so there is no good reason not to pull it out at that point and it is far easier to do this with it removed where you can see everything that is happening in the lines.