- Making a bone saddle and nut
Bone Saddle:
The intonation was sharp on this Patrick Eggle acoustic/electric guitar. 
The intonation at the saddle can only be adjusted within it's 1/8th inch thickness, so some intonation problems can only be fixed by either moving the bridge, making a new bridge, or moving the saddle slot. Rather than ship it back to England for those warranty repairs the owner decided we should do the best we could with a new saddle.
There were two adjustments I could make. The original saddle was crowned down the middle, and slightly loose so it tilted forward towards the neck. Because the intonation was sharp I needed to move the string contact points back. The new saddle should be crowned along its back edge, and also be tighter so it wouldn't tilt. (Not too tight because in an acoustic/electric the saddle has to be able to move in the slot in order to transfer sound to the pickup.)
Using sandpaper on a flat piece of marble I sand the blank flat, and close to the final thickness.

I cut it to rough length with a hack-saw, then sand close to final size with a bench disc sander. I use a radius block to shape the top so it matches the fretboard radius:
I marked the flat top with pencil so I could see where the crown was developing as I filed. When this was right I polished the top, then sanded the bottom flat and square, down to the final height.

Finished. The intonation was improved enough to save shipping it to England and back.
Bone Nut:
A customer brought in a nice guitar that he'd made from a kit. I did a few final touches, including making a new nut.
I sized the blank on flat sandpaper to it's final thickness. To mark the top shape I use a pencil that has been sanded in half. With the pencil resting on the first two frets I can trace the level and radius of the frets.
The initial shaping is done on the belt sander, just shy of the pencil lines.
This is a graduated ruler designed for marking the string slots. The thicker strings have to be slightly farther apart than the thinner ones so the spaces between them will be equal.

I make the initial cuts with my thinnest fret slot file, right on the pencil lines. Then I gradually widen the slots with wider files to match each string width.
With the nut in place and strings on I file each slot to it's final depth and width. It's important that the string slots are sloped down toward the tuning pegs. This is critical for intonation. The high point on each slot needs to be at the very front edge of the nut. I like to tilt the file about half way between the plane of the fret board and the plane of the peg head. This gives full bearing of the string as it crosses the nut.
After final shaping and polishing I glue it in with two small drops of Elmers white glue. This holds well enough but not so tight that the nut can't be removed later. The outer strings hold it in alignment while the glue dries.