The intensifying FBI probe of newly discovered emails tied to Hillary Clinton’s scandalous private server has put a bull’s eye on her stalwart confidante Huma Abedin — targeted with a warrant yesterday — who now must weigh how much assistance to give the feds as they sift through thousands of messages found on her estranged husband Anthony Weiner’s laptop.

Feds yesterday secured a search warrant for the computer, which was seized in an underage-sexting investigation of Weiner. The warrant was needed because the FBI only had judicial clearance to search Weiner’s computer for ­sexting evidence, but found copies of Abedin’s emails on it as well.

Metadata on the laptop “suggests there may be thousands of emails sent to or from the private server that Mrs. Clinton used while she was secretary of state,” The Wall Street Journal reported. In all, copies of 650,000 emails were found.

FBI Director James B. Comey announced the discovery Friday in a bombshell letter to Congress, which was decried by Clinton supporters as improperly influencing the Nov. 8 election.

Former U.S. Attorney for Massachusetts Donald Stern told the Herald it’s “almost impossible” to tell if the emails can all be scrubbed before Nov. 8, but said Abedin’s cooperation would accelerate the process.

“I think there’s a real interest at this point, given what Comey’s already done, to having more information out there,” Stern said. “And if that requires some of the participants to cooperate with law enforcement, I would hope that would be done.”

Stern added he assumes ­Abedin, who served in the State Department under Clinton, will “make her own independent judgment about what to do with the advice of counsel, but I’m sure she has a strong interest in getting all the facts out as quickly as possible so that this can be put to rest.”

The Clinton campaign has called on the feds to release all they know. But it is unclear how much detail — either exculpatory or incriminating facts — can actually be gleaned from the thousands of emails within a week. Clinton is unlikely to be questioned by the feds again before the election, legal experts said, but if she is elected the investigation could hang over her adminstration.

Clinton didn’t directly address the controversy in a stump speech yesterday, and her campaign did not respond to a request for comment.

CBS News, citing law enforcement sources, reported yesterday Abedin was cooperating with ?officials and “seemed surprised that the emails were there” on her husband’s laptop. Abedin said in a sworn deposition in June she gave the FBI all relevant devices.

The Associated Press, citing sources, reported yesterday that FBI agents on the Weiner sexting case knew for weeks about the emails potentially related to Clinton’s private server. It was not ?immediately clear what steps they took to fully advise FBI leaders. Comey said he was briefed last Thursday and agreed that investigators should take steps to review the emails for any classified information.

Pressure also is mounting on Comey. U.S. Senate Democratic Leader Harry Reid blasted the FBI boss in a letter yesterday, saying his disclosure “demonstrated a disturbing double standard for the treatment of sensitive information, with what appears to be a clear intent to aid one political party over another,” and may violate the Hatch Act.

Former U.S. Attorney for Massachusetts Wayne Budd said former Justice Department officials from both parties will be going public in the next few days scolding Comey.

“It’s fair to say that (Comey’s disclosure) would somewhat undermine the political process, since there’s no adjudication obviously likely before the election,” Budd said.