A set up is adjusting the guitar to play correctly and in tune up and down the neck. This consists of adjusting the truss rod inside the neck. The truss rod allow the technician to adjust any back bow or forward bow. Adjusting the action of the strings which means the height from the fretboard to the strings.
Setting the proper radius of the saddle or saddles to match the radius of your fretboard.
Setting the intonation. With intonation, I'm going to over simplify this explanation.
All string have a specific scale length (the length between the nut down to the saddle). The distance (usually not noticeable with the eye or even with a ruler) from the 12 th fret to the saddle on a high E is a different distance than from 12 th fret to the saddle on a low E.
Then you throw in the fact that the string is being fretted, that too is changing the length of the string, yet another variable. All strings will therefore be compensated differently due to the thickness of each string. Anyway, back to the set up. The guitar will be restrung, electronics will be spray cleaned. Tuners oiled and tightened if applicable.