Prudfit volunteered for the Union Army during the civil war and initially served in the 1st Wisconsin Volunteer Infantry Regiment. He later joined the 12th Wisconsin Volunteer Infantry Regiment. This regiment would take part in the Siege of Vicksburg and the Jackson Expedition. Proudfit became its commander in 1864, succeeding George E. Bryant. In 1865, he was brevetted a brigadier general. Proudfit was Adjutant General of Wisconsin from 1865 to 1868 and U.S. Surveyor General of the New Mexico Territory from 1872 to 1876. Proudfit served in the Wisconsin Senate in 1866 and 1867.