Rapier was enlisted from
Louisiana as a private in Captain Henri St. Paul's Company (Second Company) of the Louisiana Foot Rifles on April 22, 1861. This was later folded into Company A, 7th Battalion, Louisiana Infantry. Their first assignment was Pensacola, Florida, where they arrived on April 28 and stayed until mid-September. They were then transferred to Richmond, Virginia, where they encamped for several months in the vicinity of Centerville. The battalion was then assigned to Brigadier General Richard H. Anderson's Brigade on the Virginia Peninsula in May 1862. He served there briefly until he was ordered on December 22, 1863, to report to Admiral
Franklin Buchanan, commander of the Mobile Squadron. On arrival on December 28, he was assigned to the Mobile Marine Barracks. On August 3, 1864, Rapier and several fellow marines were ordered to reinforce
Fort Gaines on
Dauphin Island,
Mobile Bay,
Alabama, during which time he was made Major W. R. Browne's adjutant. Rapier was captured on August 8, 1864. He later escaped from prison in New Orleans on October 13, 1864, by making his way through the swamps and
bayous until he reached Mobile on November 10. He met up with Captain Fry, a relative, who gave him command of two 32-pounder guns on the gunboat
Morgan. He participated in the
Battle of Spanish Fort and the Battle of Fort Blakely in April 1865. He was on this boat until he surrendered on May 4, 1865. He was paroled May 10, 1865, at Nanna Hubba Bluff, Alabama. ==After the war==