If the markings are deep enough, some people are happy to simply coat over them and lose the contrast. I personally don't like that.
If they are deep, you can also color fill them.
Many optics are only laser marked, just through the anodizing or just altering the color of the anodizing, or using other methods of marking that the above methods ail not work with.
What I normally do is completely mask them off. Optics and rifles often have black parts that can't be coated, such as rubber or certain plastics, like buttpads and stuff, so I just bring small amounts of black through the finish, making controls of flashers, which really show carbon f they are light, black. This makes any black parts on the optic look natural. I usually make rings of black opposed to just rectangles, or i can mask with my templates and bring the shape of the pattern into it, or i cut rectangles with a pointed end to mask certain marlins in a way that defines a certain point. Examples below shoe different optics and methods done and needed and to customers' preferences.