Shortly after the beginning of the war the estate of Robert E. Lee in Arlington, VA was confiscated by Union soldiers in May 1861. The main house served as the headquarters for the Army of the Potomac and later the Army of Northeastern Virginia. In 1864 it was decided to be the location of the new military cemetery as the military cemeteries in Washington D.C. and Alexandria, VA were reaching capacity. It was also motive to put the cemetery there to remind General Lee what he helped cause. The location later became Arlington National Cemetery.
American Civil War page