The end of the Civil War was not merely a handshake agreement with life returning to normal. The balance of life for both the Union and Confederacy had been torn apart, both physically, by families, economically and socially. The reconstruction involved time and effort.
Most Confederate soldiers signed an oath of allegiance in order to gain status as a United States citizen. In 1863 President Lincoln issued a proclamation to grant pardon or amnesty to Confederates. President Johnson issued an amnesty proclamation on 29 May 1865. Under the 1865 proclamation, former Confederates who had not been pardoned in 1863, could receive amnesty. First they had to take an oath to defend the Union and Constitution, and obey federal laws and proclamations regarding slavery. These were similar to that issued by President Lincoln in 1863. The pardons issued in 1865-1867 were normally not to Confederate soldiers, but to other individuals who supported the Confederate cause.
If their property was valued at more than $20,000 they could not apply for a pardon. Persons who had broken their oath under the Lincoln proclamation of 1863, could not re-apply for pardon. It was also not extended to graduates of Annapolis or West Point who had served in the Confederacy. Civil or diplomatic agents or officials in the Confederacy and ex-Confederate governors could not apply for amnesty.
Confederate military officers above the rank of a Navy lieutenant or Army colonel were excluded. Members of the United States Congress who resigned to assist in the rebellion were also excluded. Military personnel who resigned their commissions in the Army and Navy of the United States were not allowed to apply for a pardon.
Even with all of these and more restrictions to the 1865 pardon act, President Johnson received thousands of applications. He had granted 13,500 pardons by the later part of 1867. The number of restrictions was reduced by a second proclamation issued in September 1867.
Another proclamation was issued on 4 July 1868 in which Jefferson Davis, Robert E. Lee, John C. Breckinridge and a few others were restricted from pardon. A final proclamation was issued on 25 December 1868 which granted amnesty to everybody who had participated in the rebellion.
These proclamations resulted in many records, most of which the normal researcher has never had the opportunity to check ... or never thinks to check. The records consist of affidavits, recommendations and depositions asking for pardon and oaths of allegiance. Some are more detailed than others, but they usually provide information on the applicant, his activities during the Civil War and his current status.
The original records are housed in the National Archives in Washington, D.C. However, they are also available for searching on Ancestry.com, in a newly released database of about 14,000 files.
Ancestry's database is interesting to search. I have personally found files for ancestors who did not serve as a soldier in the Confederacy, but acted in other capacities, such as a sheriff (in a Confederate state) or postmaster. In most cases, they told their account of the war and why they did not wish to enlist as a Confederate soldier.
If you do not have access to Ancestry.com, microfilm of the pardons is available through the Family History Library (LDS) and can be rented at any of their Family History Centers.
The microfilm collection, M1003 of the National Archives, is available on 73 reels of film at the Family History Library. More information film numbers can be found at FamilySearch International.
The application files are divided into three groups. The first group consists of applications submitted by persons in the South (Alabama, Arkansas, Florida, Georgia, Kentucky, Louisiana, Maryland, Mississippi, Missouri, North Carolina, South Carolina, Tennessee, Texas, Virginia and West Virginia). The second group consists of applications submitted by persons from the North and West (California, Delaware, District of Columbia, Illinois, Indiana, Iowa, Kansas, Massachusetts, Michigan, Nebraska, New Jersey, New Mexico Territory, New York, Ohio, Pennsylvania and Rhode Island). The third group are applications submitted by persons without designation of state or territory.
To make your Confederate ancestors' life story more complete, be sure to check out the Confederate Applications for Presidential Pardons. It is worth the time to search and read the applications.