Guitars have very precise geometry. The angle of the neck to the body is essential to maintain playability and the position of the bridge relative the the fretboard is critical for a guitar that is correctly intonated. Intonation basically means that the guitar plays in tune up and down the neck.
The distance from the nut (at the top of the neck) to the 12th fret has to be exactly equal to the distance from the 12th fret to the saddle in the bridge. Ok - there's a slight deviation from this rule - because of the different width of the strings, we add a small "compensation" to the distance from the 12th to the saddle. This compensation (or extra distance) is about 2.5mm on the high string and 5.5mm on the low string. This is why a guitar's saddle isn't perpendicular to the strings - instead it has a slight tilt.
But before we can mount the bridge to the body, we need to sand the base of the bridge so that it matches the curve of the top. This is easily done by just placing sandpaper on the top and sanding the bridge.
Here are some shots show the various steps involved in locating the bridge, aligning it and the routing out the slot for the saddle.
Once the bridge is mounted, the nut and the saddles are carved from Tusq - a "fake" bone material. I use Tusq because I just don't want animal products in my guitars. It performs just as well as bone and looks very similar. I adjust the nut and saddle as well as the neck until I am happy with the playbility of the guitar. This process usually takes a couple of weeks as I like to let it settle in and then do a small adjustment, rather than over adjusting too early.