Charges included more than 200 counts of criminal activity such as murder, conspiracy to use weapons of mass destruction against civilians and more.
US District Judge Lewis Kaplan approved the request, which is a common procedure when the defendant dies.
The charges included bin Laden`s role in the bombings of American embassies in Kenya and Tanzania in 1998.
None of the charges were related to the September 11, 2001 attacks on the US.
The court papers filed on Friday included a statement from a Justice Department official declaring detailed evidence that bin Laden was killed by US forces in a raid on May 2 in Pakistan.
The statement said DNA samples, facial recognition analysis and the confirmation of one of bin Laden`s wives all confirmed the identity of the al-Qaeda leader.
"These tests confirmed that the sample from the Abbottabad raid genetically matched the derived comprehensive DNA profile" for bin Laden, the official wrote in the statement. "The possibility of a mistaken identification is approximately one in 11.8 quadrillion." (*)