Drill holes can be visible and do not necessarily make the flaw less visible.  Laser drilling often doesn't improve the clarity grade.  The drill hole doesnt jeopordize the integrity of the stone, however if it fills with a foreign material it will become more visible.

Dark inclusions and imperfections are bleached, vaporized, or etched with acid which may make the diamond more desirable. 

Fracture filling is another way to improve a diamonds clarity.  A form of molten glass is infused into diamond fractures.  Fracture filling does make a diamond look better.  However, the filler can slightly lower a diamonds color.

Fracture filling does not last. Please note high temparatures and repeated cleaning can harm fillers.  Also if a diamond is exposed to UV radiation or even sunlight can discolor a filler and make it look cloudy over time.

Most jewelers will not work with treated diamonds beause of sensitity and liability.

Drill holes become permanent characterisitics All major gem labs such as GIA will give fracture filled treated diamonds one grade lower then they appear to be.  Gem labs will also report them as permanent clarity characteristics.  

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