On June 23, 1860, Alden became an assistant surgeon. During the next year he served in New Mexico, at five locations. At the beginning of the Civil War, he was captured (together with most of the 7th Infantry) on July 27, 1861, in San Augustine Springs. He was paroled and for about a year served at camps of prisoners of war at Fort Leavenworth, Jefferson Barracks, and Rouse's Point.
In July 1862, Alden travelled to Washington, where he organized the Georgetown College Hospital.[2] In October, his parole having expired, worked for the medical director of the Army of the Potomac, during which, he commanded the evacuation of wounded after the Battle of Fredericksburg from Falmouth to Acquia Creek. In Spring 1863, he travelled to Philadelphia, and was given charge of Turner's Lane General Hospital and made recorder of the Army Medical Examining Board.[5][6]
He was given the brevets of major and lieutenant colonel on March 13, 1865, for “faithful and meritorious service”[7] and on June 23, 1865, was promoted to captain in the regular corps, and later a major. In May 1867 he was transferred to the 30th Infantry, which was protecting builders of the Transcontinental railroad in Wyoming. He was on this duty and spent time at Fort D. A. Russell, Wyoming, for three years, later at Fort Gratiot, Michigan (from 1870 to 1872), then a year at Fort Porter, Fort Walla Walla (1873–1876), and a final year at Fort Townsend. Alden spent four months’ leave in1873, traveling to Europe and, in 1875, fighting in Wallowa Valley, Oregon, and later in Idaho in 1877 with a campaign against the Nez Perce.[4]
He travelled New York City in November 1877, where he would work for five years as recorder of the Army Medical Examining Board until Alden was transferred to Fort Yates. After two years, he was sent to Fort Snelling, where he served as post and attending surgeon at the Department of Dakota headquarters.[8][9]
Alden wrote Reports on surgical cases to the surgical section of the Medical and Surgical History of the War of the Rebellion and a Report on prison depot, Fort Delaware. Later, a report "on the climate of Fort D. A. Russell together with its flora and fauna was issued as a circular from the office of The Surgeon General in 1870 as was also a similar report on Fort Walla Walla in 1875. A report of surgical cases in 1871 was made the subject of a circular from the same source (S.G.O. Cir. No. 3, August 17, 1871)." An early proponent of antiseptic surgery.[10]