The definition of a well functioning machine is one that is clean and well lubricated; the guitar is no different, but what makes it dirty to begin with?
Believe it or not, the most common substance to make your guitar dirty is human skin, whether it be in the form of dust, or accumulated goo on your fret board. Common house dust is made up of 90% human skin and makes its way around as we move and continually shed it. When you remove your strings, examine the fretboard and you'll see traces of hardened goo beside the frets on the fretboard. This is skin from your fingers that has mixed with perspiration and builds up. The easiest way to eliminate it, and at the same time, make your frets last longer, is to clean the fretboard with steel wool.
Remove the strings from your guitar, using masking tape, cover your pickups, and (or) sound holes. Continue this procedure in your basement or garage as there will be filings on the floor afterwards.
(if you have a glossy maple neck, you will want to tape off the lacquer sections between the frets first.)
Using "0000" or "Ultrafine" steel wool ONLY, rub the guitar fretboard along it's full length in the direction of the grain only. Continue this for about a good 5 minutes and you will see the frets gleaming and your rosewood/mahogany/ebony fretboard will look clean as a whistle.
Now that you have removed the top layer of cells from your fretboard, you have exposed the wood to the elements. This needs to be sealed with bore oil so your neck will not dry out, causing frets to lift and the neck to become "rollercoaster". Take the bottle of bore oil or lemon oil, pour some on a clean cloth and spread it over the length of the fretboard. Let the oil sink in for about five minutes and then remove the excess with a fresh paper towel.
Your Finish
When removing dust off the finish, remember that if you dry dust it with a cloth, you are grinding the dust and dirt into the finish giving your guitar a hazy look after time.
Guitar polish is actually a cleaner and sealer, as the definition of polish is a liquid suspension that contains abrasive particles that remove microns of your finish until it is taken down to the depth of the scrapes and scuffs that were visible. A good example of a true common abrasive is Brasso. We'll just call guitar polish by it's name for the sake of familiarity. Here's how to clean your guitar in a safe way for any style finish.
1. Start with a camel hair painter's brush that you keep in your case. This is good to use on yuor headstock and under the string on your guitar's body as it will remove the dust without scraping even the most delicate lacquer finishes. After these areas are free of dirt and dust, spray a virgin piece of lint free paper towel with your guitar polish so it is moist, not wet. Wipe the guitar in sweeping motions without a lot of pressure until all the exposed area has been covered. This is done so the polish can act as a lubricant while you remove the dust and dirt with the paper towel. Discard that towel now. Using a fresh paper towel, wipe off any excess. Now that the surface is clean, repeat the first procedure as you will now be sealing the finish. We can't see it with the naked eye, but paint and finish is made up of tiny porous flakes that can let moisture through and make for an uneven surface. Sealing it ensures that your finish will remain flat and last the life of the guitar.
If your have developed swirl marks of scratches, here is the scoop. If you can feel the scratch with your fingernail, you have to have the scratch fixed by filling, sanding, and buffing. Those miracle commercials where you are duped by someone scratching a white car with a black crayon, and they tell you it was their key, and they use their "miracle cream" to remove it instantly, are pure fantasy.
If you have swirl marks or very faint scratches, you can use a Meguire's formula that Fender markets, or swirl remover that Planet Waves sells, that will remove a few microns of the finish until it reaches the depth of the scrape. Be careful to test these products on a hidden area of your instrument if it is an alcohol based laquer as they are a little more unstable than polyester and urethane finishes.
Beware that if you have not completely cleaned the guitar of contaminants, you are making new marks as you remove the old. The guitar and paper towel must be COMPLETLEY clean before polishing.