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The group has given the late actor, who died in January, the best actor accolade for his role as The Joker in The Dark Knight.
Sister Kate reportedly fought back tears as she accepted the prize on behalf of Ledger. She said: "It has been without a doubt the most difficult year, losing such a loved family member.
"We are so proud of him and humbly accept this award on behalf of his beautiful daughter [Matilda] who we will cherish forever."
The AFI paid tribute to Ledger by describing him as "the untamed spirit many of us wish we could be".
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