
David Haller |

The archer has pinpointed the invisible creature's location (which square he's in), but the creature is still *unseen* and has total concealment - the archer still has a 50% miss chance.
If the archer's bow has the Seeking quality (always recommended for high-perception archers who can't magically counter invisibility), pinpointing the square is enough: Seeking will ignore the miss chance.

Mapleswitch |
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Perception = hearing AND vision AND touch. Invisibility gives a +20 stealth to VISION. The caster does not get a +20 stealth to silent walking. A simple perception would detect the square the mage is in (unless s/he is flying, levitating, has silence going, or something similar). Beating the +stealth bonus with a perception would indicate seeing and following feet prints on the ground/body shapes moving low lying fog in the air, an insect flying into an invisible object, and would allow the zen archer to hit the mage without the 50% miss chance.
Most players and dungeon masters forget to calculate the distance factor into perception checks. (-1 perception per 10 feet you are away from the target), so the zen archer from 150 feet away would have to roll 35 (15 from 150 feet and 20 from stealth) above your stealth check roll to see you.

David Haller |

Well, a zen archer 150 feet away would have to roll a 55 - +20 to be aware of invisible creatures, +20 again to pinpoint, and +15 for distance (though there are ways of mitigating this with magic items).
If the invisible caster were also trying to actually be stealthy (ie. using a rod of silent spell or a staff of the master with the silent spell feat, and moving half speed, stealthily), the stealth check would be added to that - so we're looking at a stealth check + 55 as the archer's perception DC!
Of course, it's possible, with effort, to have a silly perception bonus (and archers need it) - my 11th level PFS ranger can hit a DC of 92 versus humans in urban terrain, for example - but invisibility remains among the most potent defenses.
(Unless the archer is accompanied by an arcane caster running See Invisibility and carrying a wand of glitterdust, in which case the discussion is moot!)