I do not have access to Federal prison lists. However, it seems remote to me that his name might appear on any list as there is no mention in his Compiled Service Record. I suggest your next step would be to post your query on "The Civil War Prisons Message Board."

Unfortunately, his name is so common that I cannot search Federal records to see if he enlisted in the Federal Army.

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Robert Smith, Private, Company B, 2nd Louisiana Cavalry, enlisted in Captain James D. Blair's Company, Vincent's Regiment, Mounted Partisan Rangers*, June 18, 1862 at Natchitoches Parish by Jas. D. Blair for the duration of the war, marked present September 14, 1862, recorded on the Jan & Feb, 1863 muster roll as: detailed as a Wagoner [having lost his horse***], last paid February 28, 1863, deserted June 13, 1863 as recorded on the July & Aug, 1863 muster roll**

* This company was also known as Company B, 33rd Regiment Partisan Rangers, and consequently became Company B, 2nd Regiment Louisiana Cavalry

** There are no surviving later muster rolls. Thus, we do not know if he later returned to his company.

*** In the Confederate Army cavalry, soldiers had to provide their own horses. Somehow his horse was lost, during the interim period he was assigned as a Wagoner, most likely driver, etc.
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Record of Events:

Company B, January & February, 1863 stationed at Battery Fusilier
Company A, December 31, 1862 to Feb. 28, 1863, stationed at Camp Bisland
F & S, July & August, 1863, stationed at Camp near New Iberia
Company C, July & August, 1863, stationed at Vermillian Bridge

The regiment at this time appears to have been posted at Forts along the line of the Opelousas and Great Western Railroad to the West of New Orleans

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Regimental Assignments:

Sept. 1862 to Aug. 1863, unattached
Jun. 1863 to Nov,, 1863 attached to Green's Cavalry, Dist. of W. La.

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2nd Regiment, Louisiana Cavalry

2nd Cavalry Regiment was organized during the summer of 1862 with men from the southern section of the state. It was assigned to the Trans-Mississippi Department and served within the boundaires of Louisiana througb the war. The unit confronted the Federals in many conflicts, but in the fight at Henderson's Hill on March 21, 1864, it had 15 officers and 192 men captured. It continued to serve, then disbanded during the spring of 1865. The field officers were Colonels James D. Blair and William G. Vincent, Lieutenant Colonel Winter W. Breazeale, and Major James M. Thompson. [http://www.itd.nps.gov/cwss/regiments.cfm]

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A Regimental webpage which delineates the battles fought, etc., is found at: http://www.acadiansingray.com/2nd%20Regt.%20Cav.htm