(NewsNation) — A federal judge has appointed Raymond J. Dearie to independently review documents seized by the FBI during their search of former President Donald Trump’s home in Florida.

Dearie, a senior judge in New York, will serve as special master in the case and review all of the approximately 11,000 documents taken — including some that were classified — and identify those that could be deemed as protected by attorney-client privilege and executive privilege. The Justice Department had asked that Dearie not be allowed to view the approximately 100 classified documents that were found during the Aug. 8 search.

U.S. District Judge Aileen Cannon also denied the DOJ’s motion for a partial stay of her order that requires prosecutors to stop using the seized documents in its criminal investigation. The Justice Department is investigating how the tranche of classified documents ended up at Mar-a-Lago after Trump left the White House, and court filings have revealed prosecutors are probing possible obstruction of justice and violations of the Espionage Act.

Trump sued the government three weeks after the search, asking that a special master be appointed, claiming his Fourth Amendment rights were violated and demanding documents be returned.

The Justice Department argued a special master was unnecessary because its own teams had already sorted out those covered by attorney-client privilege. Prosecutors also said Trump had no right to the documents because they don’t belong to him, and the Justice Department plans to appeal Cannon’s decision.

In her ruling Thursday, Cannon rejected the government’s argument that there was no way to allow an intelligence community review of the national security impact on presence of the documents at Mar-a-Lago while simultaneously putting the criminal investigation on hold.

“The Government’s submissions, read collectively, do not firmly maintain that the described processes are inextricably intertwined, and instead rely heavily on hypothetical scenarios and generalized explanations,” she wrote.

She instructed the lawyers and Dearie to first prioritize the classified documents and set a deadline of Nov. 30 to complete the review, more than a month after the DOJ’s proposed deadline of Oct. 17. Trump will have to pay 100% of the legal fees associated with the review.

Cannon also ordered the government to provide Dearie with the search warrant and the redacted version of the probable cause affidavit.

While the documents are off-limits for prosecutors, Cannon clarified the DOJ could take other steps to continue its investigation, such as “questioning witnesses and obtaining other information about the movement and storage of seized materials, including documents marked as classified, without discussion of their contents.”

She also said the department was free to brief Congressional members on national security implications.