Andrew Weissman, who served as a prosecutor on special counsel Robert Mueller‘s Russia probe, believes both men – convicted in that investigation – may be brought before a grand jury again and asked to testify.
Mr Manafort, the president’s former campaign manager, was jailed in 2019 for financial crimes.
Meanwhile, Mr Stone, a former adviser to the president, was convicted of multiple offences, including obstructing the House investigation into whether the Trump campaign colluded with Russia during the 2016 election campaign.
He was sentenced to 40 months in jail but had his sentence commuted in July, a day before he was due to be locked up.
Both have now had their convictions struck out by Mr Trump, who is issuing a slew of pardons to ex-aides caught up in the scandal, as he prepares to leave the White House in January.
Speaking to MSNBC on Thursday, Mr Weissman said that neither man is fully out of the woods yet, and will have no protection against future charges.
“You cannot be pardoned for future crimes and each of those people, Roger Stone, Paul Manafort, Michael Flynn, has evidence in their head,” he said.
“They have information that a grand jury could seek, they can all be given grand jury subpoenas, required to testify in the grand jury.”
Michael Flynn, the president’s first national security adviser, was pardoned in November having been convicted for twice lying to prosecutors about his contacts with Russia.
Mr Weissman added: “If they then lie before the grand jury, which is a new crime, and that happens after 20 January, there is no president Trump at that point to give them a get out of jail free card.
“And so all of this effort by the president to shield his friends and allies and potential conspirators will be for nought.
“Because all of these people can be in that trick box of being put before the grand jury where they either have to tell the truth or they risk being prosecuted for a new crime of perjury and obstruction of justice”.
The president on Wednesday night announced a further two dozen pardons, a move that has been criticised by those within his own party.
He has now granted clemency to nearly 50 people in the past week. Charles Kushner, the father of his son-in-law, Jared, was among the others who had their crimes excused.