A federal judge on Wednesday appeared to reject the majority of the arguments made by former Trump campaign chairman Paul Manafort Paul John ManafortOur Constitution is under attack by Attorney General William Barr Bannon trial date set in alleged border wall scam Conspicuous by their absence from the Republican Convention MORE in his lawsuit seeking to limit the scope of Robert Mueller Robert (Bob) MuellerCNN's Toobin warns McCabe is in 'perilous condition' with emboldened Trump CNN anchor rips Trump over Stone while evoking Clinton-Lynch tarmac meeting The Hill's 12:30 Report: New Hampshire fallout MORE's special counsel investigation, Reuters reports.

U.S. District Judge Amy Berman questioned Manafort's attorney on the legal reasoning behind the former Trump aide's argument that Mueller's investigation has overstepped and should be shut down.

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“I don’t really understand what is left of your case,” Berman reportedly told Manafort's attorney, Kevin Downing.

Manafort's civil lawsuit relies in part on a law called the Administrative Procedure Act, which dictates how federal agencies write regulations. Manafort claims that Deputy Attorney General Rod Rosenstein Rod RosensteinDOJ kept investigators from completing probe of Trump ties to Russia: report Five takeaways from final Senate Intel Russia report FBI officials hid copies of Russia probe documents fearing Trump interference: book MORE's order last year appointing Mueller violated Justice Department policies.

He also claims that Mueller does not have the authority to investigate allegations that predate his time on Trump's campaign.

Mueller's team in a filing on Monday rebutted Manafort and asked the court to dismiss his lawsuit, saying it "lacks merit."

"None of the authorities Manafort cites justifies dismissing an indictment signed by a duly appointed Department of Justice prosecutor based on an asserted regulatory violation, and none calls into question the jurisdiction of this court," the special counsel's office wrote.

In a heavily redacted memo also filed Monday, the special counsel's office revealed that Rosenstein explicitly gave Mueller the authority to investigate Manafort's Ukraine work, along with whether he "committed a crime or crimes by colluding with Russian government officials" during the 2016 presidential race.

Manafort is charged with money laundering and tax fraud related to his lobbying work for a pro-Russia political party in Ukraine. Mueller's team alleges that Manafort and his business associate, Richard Gates, attempted to conceal the money they made from that lobbying work from U.S. officials.

Gates pleaded guilty to two charges earlier this year and is now cooperating with the special counsel's investigation.

Manafort has pleaded not guilty and steadfastly denies both the charges and broader allegations of collusion with Russia during the 2016 race.

"I had hoped and expected my business colleague would have had the strength to continue the battle to prove our innocence. For reasons yet to surface he chose to do otherwise. This does not alter my commitment to defend myself against the untrue piled up charges contained in the indictments against me,” Manafort said in February.