Possession of marijuana under federal law is a misdemeanor and by paying the ticket, he is essentially admitting his guilt (much like when you pay a speeding or other traffic ticket). The conviction would be on his record. He can try to challenge the ticket in court or try to make a deal with the prosecutor that would keep the charge off his record. It is unfortunately a lot more difficult at the federal level than the state level. Many states have programs where a first offender completes some community service and a drug education class and the charge is dismissed but most federal courts do not have comparable programs. He may want to consult with a federal lawyer if he can because technically by challenging it, he could open himself up to additional penalties that he would not face by paying the prepaid amount on the ticket.
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