Her fitting out as Manassas was completed at Algiers, Louisiana; her conversion to a ram of a radically modern design made her the first ironclad ship built for the Confederacy.

Covered with 1.25-inch (32 mm) iron plating, her above-water hull was reshaped into a curved "turtle-back" form; at its lowest when fully loaded, the hull projected only 6+1⁄2 feet above the waterline, not counting her smokestacks (surviving accounts and period illustrations vary showing Manassas was equipped with either a single or two side-by-side smokestacks, possibly slanted back at a rakish angle).

Her bow was fitted with a pointed iron ram to stave holes in Union vessels, and she also carried a forward-firing cannon behind a single gun port with an armored shutter.

"[3][4][5]: 68–9 Commissioned as a Confederate privateer on 12 September 1861, Manassas was seized soon afterwards by Flag Officer George N. Hollins, CSN, for use in the lower Mississippi River.

In the action Manassas attempted to ram USS Pensacola, which turned in time to avoid the heavy blow and delivered a full broadside at close range.

With the launches Mosquito and Sand Fly, she was placed under Lt. W. H. Murdaugh, CSN, who was seriously wounded in the Federal attack on Fort Hatteras the next day, and was unable to assume his command.