The big three of the Confederacy at the end of the war were:

President - Jefferson Davis Vice President - Alexander Stephens General of the Confederate Forces - Robert E Lee

Both Davis and Stephens were imprisoned albeit for a short period (2 years for Davis and 5 months for Stephens). They were also barred from holding office or to vote. Lee was not imprisoned however he had his farm in Arlington seized; which later became Arlington National Cemetery.

In 1868, President Johnson pardon all Confederates in order to bring reconciliation between the North and South, however with the exception of Stephens (who later became a House Representative) , Davis and Lee did not have their citizenship restored. It wasn't until 1975 and 1978 were their citizenship restored, posthumously.

The main goal of Reconstruction was reconciliation and reunification. Giving the Confederates harsh punishments was never the objective.