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Think you have to do something bad for the government to take your fingerprints? Well you dont, I have to go today and give them up to the police so I can get my security clearance. Guess if i get the nerve to go on a crime spree i'll have to burn them off first (or wear gloves).
"Don't worry Mr. Reinhart, we've known you for a long time and so has the government. We just requested your fingerprints so that we can inconvenience you."
I have to file my prints for my insurance license. They also do a FBI background check before you can sit for their tests. As long as you don't do anything bad, you'll be ok!