Cruz, a narcotics investigator, had been helping West Whiteland Township police investigate a suspected methamphetamine lab in August 2009 when he detained Zachary Bare, then 22, in an Exton home Bare shared with his mother.
Bare was handcuffed and lying facedown on his kitchen floor when Cruz allegedly stomped on his head. In reports describing the incident, police described seeing the trooper pressing the suspect's head into the floor, and then blood and teeth spilling onto the floor.
Bare was never charged with a crime and later filed a private criminal complaint against the trooper.
When a state grand jury declined in October 2011 to return any charges against Cruz, Bare's lawyer called it "a whitewash" to protect the trooper.
Cruz, of Oxford, has been charged with depriving Bare of his civil rights. He has been suspended without pay, his lawyer, Christian Hoey, told Magistrate Judge Lynne A. Sitarski.
The judge released Cruz on $50,000 bail and ordered him to surrender any guns in his home. She also said that Cruz, a Navy veteran who has served combat tours of duty in the Middle East, may participate in Reserve drills in Italy.
Bare's lawyer, Joseph P. Green Jr., declined to comment on the new federal charges, saying he had not yet seen them. Green also said he was unsure whether Bare knew about the new charges.
Asked if the federal case represented vindication for Bare, Green said: "If this is vindication for anyone, it's for the honorable and dedicated police officers in West Whiteland Township who saw wrongdoing and did the right thing."
Last year, Bare reached an out-of-court civil settlement with Cruz over the incident. Green said he could not discuss that settlement.
Ten months after the alleged assault, Bare pleaded guilty in Chester County to an unrelated criminal mischief charge, records show. He was sentenced to probation but later briefly jailed for violating the terms of that probation.
Contact John P. Martin at 215-925-2649, at email@example.com or @JPMartinInky.