What are the factory specifications for my PRS SE guitar setup?

• First, once the strings are thoroughly stretched, tune the instrument to pitch. Repeat stretching and tuning the instrument.
• Then, adjust the truss rod relief, and re-tune the instrument.

Using a capo at the first fret, measure the distance from top of fret to bottom of string while depressing the string at the 1st and last fret: Relief for PRS SE guitars should measure .3/64" - .6/64" (.1mm - .3mm) at the 8th fret. 

Once the relief has been set, re-tune the instrument. The measurements for string height should be as follows (measure from the top center of the fret, to the bottom of the string):

6 String

• Treble side string height 1st fret: .64/64” - 1.5/64" (.2mm - .6mm)
• Bass side string height 1st fret: 1/64” - 2/64" (.4mm - .8mm)
• Treble-side string height at 12th fret: 1.8/32" - 2.3/32"  (1.4mm -1.8mm)
• Bass-side string height at 12th fret: 2.2/32” - 2.4/32" (1.5mm - 2mm)
• Floyd Rose Treble side string height 1st fret: .6/64” - 1.5/64" (.2mm - .6mm)
• Floyd Rose Bass side string height 1st fret: 1/64” - 2/64" (.4mm - .8mm)
• Floyd Rose Treble-side string height at 12th fret: 1.8/32" - 2.3/32"  (1.4mm -1.8mm)
• Floyd Rose Bass-side string height at 12th fret: 2.2/32” - 2.4/32" (1.5mm - 2mm)
• String height should escalate in value from Hi E to low E 

7 String

• Treble side string height 1st fret: .64/64”- 1.5/64" (.2mm - .6mm)
• Bass side string height 1st fret: 1.2/64” - 2/64" (.4mm - .8mm)
• Treble-side string height at 12th fret: 1.8/32" - 2.3/32"  (1.4mm -1.8mm)
• Bass-side string height at 12th fret: 2/32” - 2.5/32" (1.5mm - 2mm)
• String height should escalate in value from Hi E to low B

Adjusting Your Action | Tips From The Tech Center | PRS Guitars - YouTube

We consider these measurements to be a "factory specification" action height. You can adjust to taste.