Anyone charged could be arrested as soon as Monday, reports CNN.
The documents, approved by a federal grand jury in Washington, are sealed under orders from a federal judge, the network said.
It is not known what the charges are at this time or who they relate to, reports Reuters.
Only hours before the news Trump had tweeted it was “commonly agreed” that there was no evidence of collusion.
The Washington Post reported that “documents and other materials were seized” during the raid on July 26.
One day before, Manafort had met with Senate Intelligence Committee investigators to discuss a meeting between a Russian lawyer and members of Trump’s campaign team that took place during the 2016 presidential election.
Manafort “answered their questions fully,” their spokesman said.
On June 27, Manafort retroactively registered as a foreign agent thanks to $17.1 million his firm was paid from 2012 to 2014 for lobbying work he did on behalf of a pro-Russian political party in Ukraine.
Fox’s Sean Hannity, Trump’s softball interviewer of choice, appeared to be stretching for an adequate explanation of the developments.
Mueller’s team is reportedly also looking into a dossier containing explosive, unverified allegations regarding Trump and his associates, compiled by former British spy Christopher Steele for the research firm Fusion GPS.
US intelligence agencies concluded in January that Russia interfered in the election to try to help Trump defeat Democratic candidate Hillary Clinton through a campaign of hacking and releasing embarrassing emails, and disseminating propaganda via social media to discredit her campaign.
Mueller is investigating whether Trump campaign officials colluded with those Russian efforts.
He is also examining other possible crimes, including obstruction of justice, money-laundering and tax evasion.
Peter Carr, a spokesman for Mueller, declined to comment to Reuters about the CNN report on Friday.
Trump, a Republican who was elected president last November, has denied allegations that his campaign colluded with Russians and condemned investigations into the matter as a witch hunt.
The Kremlin has denied the allegations.
Mueller was appointed by Deputy Attorney General Rod Rosenstein in May to investigate possible coordination between the Trump campaign and Russian officials during the 2016 presidential election.
This followed President Donald Trump’s controversial decision to fire FBI Director James Comey amid the agency’s investigation into the campaign connections.
Mueller is a former prosecutor and served as FBI director from 2001 to 2013.
As Special Counsel he has sweeping powers and the authority to prosecute any crimes he uncovers.
Mueller’s broad mandate gives him not only oversight of the Russia probe, but also “any matters that arose or may arise directly from the investigation”.