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Blacken the scratch, wait about 15 seconds, then rub on the mark with your thumb.

If you just touch the Sharpie to the black, it will be a little shiny (unless you want it shiny) and obvious.

If you wait a few seconds, then rub on it, the rubbing will take away the shine without removing the black from the scratch, and leave a dull surface. Looks much more natural.

Mike
 
You could try a product called Aluma Black It is made by Birchwood Casey works great on Aluminum. Just be sure you degrease the surface real good first. 

And never re-dip the Q-tip into the bottle because once you touch the Aluminum with the Q-tip it starts a reaction with the chemical and you could ruin the chemical if you need to reapply use a new Q-tip.
 
Those Sharpie-looking pens for furniture work much better than Sharpies.

They usually come in several shades, from beige to dark brown to black.

They do not seem to evaporate like Sharpie does.

I bought a set to retouch some of my home furniture, then curiously applied it on an aluminum surface--I was surprised of the result 👍

Buy them from Home Depot or from any hardware stores.