He continued with the Army after the war, using his expertise as assistant to the chief engineer in Washington, DC and at a post on Lake Erie.

Promoted to captain of U.S. engineers, Foster was in command of the garrison at Fort Moultrie when the Civil War began.

Foster was appointed a brigadier general of volunteers on October 23, 1861, and commanded the 1st Brigade in Maj. Gen. Ambrose Burnside's North Carolina Expedition.

After General Burnside was transferred to Virginia, Foster assumed command of the Department of North Carolina.

In December, Foster led the Goldsborough Expedition won two minor battle at Kinston and Goldsborough against inferior confederate forces led by brigadier general Nathan G. Evans, resulting in the shutdown of the vital Confederate supply line of the Wilmington and Weldon Railroad for merely two weeks.

After President Abraham Lincoln issued the Emancipation Proclamation freeing all slaves in rebel territory, in April 1863 Foster appointed Horace James, an experienced Congregational chaplain, as "Superintendent of Negro Affairs for the North Carolina District."

Foster directed James to settle the people, give them farming tools and prepare them for a "free and independent community.

"[1] By 1864, 2,200 freedmen lived on Roanoke Island, settled on individual household plots, and working for pay for the Army.

Due to President Andrew Johnson's returning lands to Confederate landowners, the colony was abandoned.

After the war, Foster remained in the army, serving as the Assistant Commissioner for the Freedmen's Bureau of Florida from June to December 1866.

During his tenure there, Foster place five Florida counties under martial law after the unpunished murders of several freedmen.

From 1871 until 1874, he was assistant to the Chief of Engineers in Washington, D.C. His final post was as superintendent of the Harbor of Refuge on Lake Erie.