I am using my drone for photogrammetry and I can not figure out if the Phantom 3 Pro uses its flight altitutde of 0' from sea level or from take off point. If it is from take off point then how can I zero it each time?

The only height the Phantom knows is Home = zero
It has no way of knowing where sea level is and there's no way to zero it.

labroides@yahoo Posted at 2015-12-28 15:35
The only height the Phantom knows is Home = zero
It has no way of knowing where sea level is and the ...

interesting. Okay thank you.

In the latest version of the firmware the phantom records GPS elevations in EXIF. Previously this was barometric altitude above take-off point.
GPS elevations are notoriously inaccurate.
However, if you fly at a constant elevation over your take off point and average a lot of images you'll be able to get a more accurate representation of absolute altitude. (haven't tried this yet as I'm still on 1.4.10

Edit: I do believe it still records baro altitude somewhere

It counts the altitude from take off point, but not from the sea level