Surface reaching fractures containing dirt have long been boiled in acid or bleached to remove unwanted inclusions. About 10 years after the invention of the laser, the first laser drilled diamonds started trickling into the labs. Crowningshield mentions in a 1970’s G&G article that he had heard rumors of laser drilled diamonds for several years.
A laser is used to create a tiny channel from the surface of the gem to an inclusion. Acids are then used to either bleach or remove the inclusion, thus enhancing the diamonds’ clarity. The drill hole may or may not be filled after the removal of the inclusion has been completed.
Identification shouldn’t be too much of a problem, proper inspection with a microscope should do the trick. Note that even melée sized diamonds can be drilled so don’t just investigate the center stone of an item!