Federal War Department General Orders #85, #98, #104, and #109 directed all members of the US military establishment to provide government transportation for the POWs and civilian detainees released under these various general orders to a point nearest their homes that could be reached by water and/or rail. When you examine the Oath of Allegiance card in their Compiled Military Service Records, you will see a specific line stating the released man's place of residence. It is almost always a county in a particular state. These generals orders applied to all Federal POW camps including Fort Delaware and Hart's Island on the east coast.
I created a time line with notes on the subject of "Going Home" which is posted on the Fort Delaware Society website at http://www.fortdelaware.org/Going%20Home%20-%20The%20War%20is%20Over.htm
Let me know if you have any specific questions pertaining to your particular research.