In April of the following year, Alden passed the examination necessary to enter the United States Medical Corps, and became a contract surgeon.

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 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.

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.

[3] 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.

[9] After three years at Fort Snelling, Alden was transferred to the United States Military Academy in 1887, where he worked there, and served as president of the Army Medical Examining Board at the same time.

"[3] In 1891 Alden (who had been promoted to lieutenant colonel on November 14, 1888), was transferred to St. Paul, Minnesota, where he assumed medical directorship of the Department of Dakota.

[7] In August 1892, Alden began working in the office of The Surgeon General and was in charge of the Hospital Corps, as well as the division of supply.

[10] As James M. Phalen wrote "During the greater part of his Washington service he was again the president of the board for examination of candidates for the corps.