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From 2002 until 2005, he served with the Department of Justice as an Assistant United States Attorney for the Eastern District of Virginia.
In April 1998, Virginia's U.S. senators Chuck Robb and John Warner recommended Lee for appointment to the United States District Court for the Eastern District of Virginia, to fill the seat vacated when Judge James C. Cacheris took senior status.
From there he moved to the Eastern District of Virginia; there he worked on the prosecutions of John Walker Lindh, the American who fought alongside the Taliban in Afghanistan; and Zacarias Moussaoui, the convicted al-Qaida operative who alternately claimed and denied a role in the September 11 attacks.