The USA never had to create a list of "enemies of the United States." The CSA accomplished that by ratifying the articles of secession from the USA. Since the USA made no such list, no entities needed to be removed from that list.

The CSA never formally surrendered. The surrender at Appomattox was a military surrender of one army to another army.

After the conflict ended, Lincoln wanted to speedily reintegrate the South back into the Union; his plan was quite lenient, since his goal was the rapid restoration of the USA to its pre-war condition. However, Lincoln was assassinated, and the Reconstruction plans that followed were quite a messy affair in many respects. The general outline was Union military forces set up governments in the South which would rule the area until replacement governments could be created by Southerners. These new governmental bodies must accept reintegration with the USA and the 14th Amendment which gave citizenship status to all formerly enslaved persons and voting rights to all formerly enslaved men. These requirements had to be met before the rebel states were permitted to rule themselves or to send representatives back to the US Congress to have a voice in deciding federal-level affairs.

Looking at the situation broadly:

1. The CSA never signed a peace treaty with the USA.
2. The CSA ceased to exist as a political entity with the governmental overthrow of the US Army.
3. The Southern states were permitted to rejoin the Union if and only if they accepted the military defeat and the change in state and local governments (and some other restrictions, such as thousands of Confederate men barred from voting and holding political office for a time); they did choose to accept those conditions.

Because of the above, even though there was technically never a peace treaty signed between the CSA and the USA, the rebellious states were offered and accepted forgiveness under specific conditions, and there are no "enemies of the USA" from the Civil War era.