The Trump administration on Friday moved to sweep away most of the remaining vestiges of Obama administration prosecutors at the Justice Department, ordering 46 holdover United States attorneys to tender their resignations immediately — including Preet Bharara, the United States attorney in Manhattan. The firings came as a surprise — especially for Mr. Bharara, who has a reputation for prosecuting public corruption cases. In November, Mr. Bharara met with then President-elect Donald J. Trump at Trump Tower in Manhattan and told reporters afterward that both Mr. Trump and Jeff Sessions, who is now the attorney general, had asked him about staying on, which the prosecutor said he expected to do. But on Friday, Mr. Bharara was among federal prosecutors who received a call from Dana Boente, the acting deputy attorney general, instructing him to resign, according to a person familiar with the matter.