On May 29, 1865, President Andrew Johnson issued a Proclamation of Amnesty and Pardon to persons who had participated in the rebellion against the United States. There were fourteen excepted classes, though, and members of those classes had to make special application to the President.
Lee sent an application to Grant and wrote to President Johnson on June 13, 1865:
Being excluded from the provisions of amnesty & pardon contained in the proclamation of the 29th Ulto; I hereby apply for the benefits, & full restoration of all rights & privileges extended to those included in its terms. I graduated at the Mil. Academy at West Point in June 1829. Resigned from the U.S. Army April '61. Was a General in the Confederate Army, & included in the surrender of the Army of N. Va. 9 April '65.
Lee sent his request for a complete individual pardon, along with an oath of allegiance, to President Andrew Johnson in 1865, and his application for amnesty encouraged many other former members of the Confederacy's armed forces to accept restored U.S. citizenship. However, the application was delivered to the desk of Secretary of State William H. Seward, who, assuming that the matter had been dealt with by someone else and that this was just a personal copy, filed it away. Lee took the lack of response to mean that the government wished to retain the right to prosecute him in the future. (Lee's right to vote was restored in 1888). Elmer Oris Parker, an employee of the National Archives, found the oath of allegiance in 1970 among old State Department records.