A gun can be identified through ballistic fingerprinting assuming they find the gun before much wear has occurred on the moving parts of the gun. The classic example is the cops recovering slugs from a victim's body and finding a gun nearby that was apparently tossed away. The bullets test-fired from the recovered guns will be bullets fired right after the gun was used to kill somebody; the marks from the rifling on the bullets should be identical.
Now if you were to put two thousand rounds through the gun and then checked bullet #2,001 to the slug recovered from the victim, your case is much weaker because of the wear and tear that the rifling has been through.
Barrels can also be manually modified; deliberately damaged by a file to destroy evidence, for example. People who home-gunsmith also do stuff to improve the accuracy of their guns by polishing the rifling using various methods. The example below is called "fire lapping", performed by coating a few dozen bullets in increasingly-fine abrasive powder and shooting them down the barrel.
http://www.ktgunsmith.com/firelapping.htm
And people use other things to scrub copper, lead, and powder residue from the barrels of their guns. Bronze-bristle brushes, fine steel wool, various cleaning chemicals.
I suppose somebody could also soak a barrel in battery acid to modify the ballistic fingerprint.
Finally, the easiest thing to do is simply buy a replacement barrel. Less than $100 gets you a brand-new Glock barrel. Ones for a .45 auto start at about $60.
Same thing goes for "microstamping".
Both systems also require that the person the gun is being registered to is the same as the person pulling the trigger. It depends on a chain of traceability that ends with the shooter. Obviously, this is difficult to achieve!
The system would only work under the following conditions:
The registered owner of the gun was the shooter, the gun was shot very little before being used for murder, and the gun was not modified.
And in those situations, the murder was probably a crime of passion or anger and there was a boatload of other evidence such that a ballistic match was merely a minor bonus.
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