Two Manhattan cops doctored reports and lied under oath to hide the fact that they made unlawful stops and searches and illegally detained people, according to a scathing indictment.

Sgt. William Eiseman, 41, and Officer Michael Carsey, 29, yesterday pleaded not guilty to charges of perjury, offering a false instrument for filing, and official misconduct.

Eiseman, who trained rookies, was fingered in four alleged incidents of misconduct between 2007 and ’08 while with Manhattan North.

Carsey is charged in connection with one of those incidents, an allegedly illegal apartment search that yielded drugs and guns.