So the Zen Archer's "Trick Shot" ability allows you to spend 3 ki points to ignore total cover and "even fire arrows around corners" with the only limitation being that the arrow must still be able to reach the target and thus a target inside a building with no open windows or doors cannot be targeted.
Now how does this interact with actual targeting? You don't know which square they're in, you don't even know if they're there. In a building, they can be in any room and the perception check to know where they are can easily reach 40-150 depending on wall thickness, distance, etc. So do you need to know where they are, merely know that they exist within the range of your bow, have had former line of sight on them?
You do need to know where they are somehow though - which square in PF terminology. Besides attempting impossible perception DCs things like scrying or just being told by someone inside the building should work.