I matched the milling bit size to the fret wire that I use – a 0.025" bit for the ukulele fret wire I used.
Using a 1/8" bit, I then cut the holes for the tuners to go through (as well as the pocket for the strings to be pulled down just past the bridge), the slots for the bridge and nut to rest in, and the outline of the instrument.
Once the instrument is cut out, you can place your frets into the slots that were cut. I cut the fret wire to be slightly wider than the neck, then tap them in one at a time with a plastic mallet. The goal when doing fret work is to make each fret as you go towards the end of the neck be slightly higher than the one in front of it (so they form a sort of amphitheater). If this is not done well, the notes will not come out clearly because the string will hit the fret in front of the one you are pushing.
Once the frets are in place, you can cut off the extra bits so they are not sticking off of the neck. I then squeeze some cyanoacrylate down the side of the milled slots to make sure they stay in place.
Once it is cut out, you can start printing the saddle (in the middle of the body where the bridge usually is) and nut (at the end of the neck). The string spacing can be uniformly spread out over the width of the neck, but the height of the pieces should be customized based on how well your frets work. If you are experiencing buzz on the frets, you can make the saddle a bit higher.
You can view my onshape project with bridge and saddle designs here:
The final step before stringing up the instrument (after adding the tuners to the holes) is to drill holes for the strings to be held in. I used a 1/16" bit and drill at an angle to make the strings easier to thread. For the end of the neck, I go from the top face of the neck just beyond the nut through to the end of the instrument at the tip of the neck. The to hold the strings down onto the saddle, I drill a hole just past the slot for the saddle diagonally into the cut out pocket so the string gets threaded through them before being wound around the tuners.