The Confederates were all US Citizens. But they took up arms against the US, which is the very definition of treason (that word gets thrown around too loosely), such that the established judicial structure is neither appropriate or can be reasonably employed.
Until they seceded, then they now longer owed any loyalty to that corrupt cesspool that Washington DC had become. (Still is.)
But they took up arms against the US, which is the very definition of treason...
None were charged with Treason. Not even Jefferson Davis, the president of the CSA.
As Chief Justice Salmon P. Chase said at the time, "Secession isn't rebellion."