Your guitar’s bridge saddle is the most significant piece of the puzzle when it comes to raising or lowering action (the distance between your strings and the fingerboard). Most modern guitars have a drop-in saddle that can be removed when the strings are off. If you have a vintage-style through-cut saddle, changing the height is best left to a pro.
After the truss rod is set correctly and your nut slots are filed properly, saddle height can be adjusted, if needed. First, take some action measurements at the 12th fret on the two outermost strings while your guitar is strung up to pitch. I like to measure from the top of the fret to the bottom of the string in 1/64-inch increments. Since action should be set relative to how you play, I’ll leave the specifics to you and the manufacturer of your guitar. The average string action of the guitars I set up is 3/32 inches on the bass side and 1/16 inches on the treble side. It is important to note that to change your action height at the 12th fret a certain distance, you must multiply that number by two to find the height to raise it at the saddle.
Before you decide whether or not to make an adjustment you should also consider that your saddle must fit deep and snug in the slot without wiggle room, that the saddle top radius should match that of your fingerboard, and that the desired saddle height should probably not average less than 1/32 inch or more than 3/16 inches above the bridge. Also, if your guitar has an undersaddle pickup, shimming the saddle may change the way it functions.
To slightly raise your saddle in a pinch, any hard flat material will do. Cutting up an old credit card into strips as wide as your saddle slot works nicely. For long-term saddle shims, hardwood veneer strips work great, and bone saddle shims are also available.
To lower your saddle, all you need is a pencil and straightedge to mark your saddle and a file and bench vise to remove material. If you don’t have access to a bench vise, a nice flat counter top and some coarse (80 grit) sandpaper will also work. It’s easiest to take material off the bottom of the saddle, because it’s flat. You should only take material off the saddle top if you want to change the top radius or smooth away string wear. Once you’ve decided how much to remove from the bottom of the saddle, mark the saddle under the low and high strings and connect them with a straight line. Then file or sand away the extra material until you hit your line, checking periodically to make sure the bottom is still square to the sides. To make sure the bottom of the saddle is truly flat, you can run it back and forth over some 120 grit sandpaper on a flat surface. This step is especially important for maintaining string balance if you have an undersaddle pickup.