One of the few Northern-born Confederate generals, he led the reserve troops of the state of Florida and helped win one of the South's last victories of the war at the Battle of Natural Bridge.

He was a veteran of the Mexican–American War, serving in the army of Zachary Taylor and was awarded by the government for his service with 40 acres (160,000 m2) of land in Florida.

On August 2, 1864, Miller was promoted to brigadier general and appointed to organize and coordinate the state's reserve troops as the new commander of the Florida District.

He raised and commanded the 1st Florida Reserves, a regiment recruited to help defend the state, as most of the regular Confederate troops were serving elsewhere.

His most prominent action came at the Battle of Natural Bridge in March 1865, where he served as the tactical field commander in defeating Union forces under John Newton.