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A pair of prominent critics of President Trump secured significant court wins on Monday when a US judge threw out the government's charges against them.

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have argued fiercely that they are not guilty, asserting that the president and justice department are simply targeting them for retaliation.

Federal Judge Cameron Currie dismissed the indictments in their cases due to prosecutor Lindsey Halligan's improper appointment as federal prosecutor. However, she left the door open for the federal authorities to try again.

• Judge dismisses cases against ex-FBI director Comey and NY attorney general James
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• What is ex-FBI director James Comey charged with?

Comey acknowledged that possibility after the decision, stating he thinks the former president will probably target him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the final word on this matter.

But the DOJ faces significant hurdles to effectively try both after this setback, and experts are reluctant to forecast what could occur next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, stated Professor Kay Levine, Emory University School of Law professor.

Might the justice department appeal?

The Department of Justice can challenge the judge's decision before a federal appeals court. In this case, that would be the Fourth Circuit Appeals Court.

US Attorney General Pam Bondi indicated she would pursue this option, vowing to use all legal means, including an expedited appeal.

In other cases, the former administration has aggressively appealed unfavourable rulings, moving cases from lower courts and sometimes accelerating its petitions up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to keep fighting any further politically motivated charges through every lawful means available.

In the event of an appeals process, the justice department likely would have its own lawyers argue the case, making Halligan's involvement in the appeal uncertain.

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with making false statements to Congress and obstructing justice. Federal prosecutors charged James with financial fraud and providing false information to a financial institution.

Both pleaded not guilty. In addition to arguing Halligan's appointment was invalid, both also asserted to be targets of retaliatory legal action.

With the original indictments thrown out (although appeals might alter this), the DOJ might try to convene fresh grand juries and secure new indictments.

As far as everything I've seen, a different attorney could bring James' case to a new grand jury and get a new indictment, stated Professor Levine.

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complex process – certainly in Comey's case.

It's clear that it will be hotly contested, whether Mr Comey's case can be recharged if a properly assigned attorney is appointed and is able to secure an indictment.

He characterized the complex web of attorneys, courts, and legal filings involved as a procedural morass with no easy solutions.

It could be more difficult for the DOJ to try to bring the identical accusations against James Comey.

One problem is the legal time limit – the deadline that prosecutors had to charge Comey for these particular claims – which ended at the close of September. However, the dismissal of the charges would trigger a half-year extension for the DOJ to bring the case again.

Still in that case, his lawyers said it intends to argue the government is out of time.

The decision further indicates that since the indictment is void, the time limit has run and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

In both decisions on the indictments against Comey and James, Judge Currie was blunt: Halligan's appointment was improper.

Judge Currie wrote in the James ruling that the Attorney General's attempt to install Ms. Halligan as Interim US Attorney for the Virginia Eastern District was invalid.

Therefore, Halligan had no lawful authority to file the charges, she wrote.

Federal prosecutors are nominated by the US president and need US Senate confirmation. US laws govern how individuals can be appointed on a temporary basis, but Judge Currie found that Halligan's assignment had violated these laws.

This makes Halligan's position on future cases against both individuals, once more, uncertain.

The ruling also could cast a shadow on other cases Halligan has brought in the Virginia Eastern District where she works.

But Bondi said on that day that she designated her a special federal prosecutor and praised her work as excellent.

The White House stood by its stance that Halligan was lawfully appointed, spokesperson Karoline Leavitt told the press on Monday.