Following Gettysburg, Munsell took part in the Battle of Kelly's Ford, the Battle of Mine Run, and the Battle of Manassas Gap. He then received an extended furlough to attend the Free Military School in Washington, D.C., where he left as a First Lieutenant. He then rejoined his regiment and took part in the Battle of Cold Harbor, the Siege of Petersburg, and the Second Battle of Deep Bottom. In the latter fight, Munsell was captured and held as a prisoner of war until his release in 1865. He returned to his company yet again, now as a Captain.