Assuming You have a completely flat base (within 0.00015") and you want to align a column about 30" high exactly vertical with respect to a machined/ground face with two reference edges (recessed cut out for mounting a linear guide). What would the best approach be to determine the alignment to about 0.0005" ?
Don't forget to aircondition the room, keep it out of sunlight, don't let the A/C or heater blow on it. Keep the temp as constant as possible - ditto that for the checking gages.
Allow the machine to become thermally stable for 48-72 hours before you start the leveling process - ditto that for the gages.
You may also want to mount in on a big thick deep slab that is NOT connected to the surrounding flooring.
If you're trying to hold tenth's in squareness, even the slightest machining load could knock it out of square. How so??? We've measured 1-2 tenths deflection in 2" dia, 26" long billets by simply resting our elbow on them. Just my $0.02.