Colonel Thayer's time at West Point ended with his resignation in 1833, after a disagreement with President
Andrew Jackson. He was elected an Associate Fellow of the
American Academy of Arts and Sciences in 1834. Thayer returned to duty with the
Army Corps of Engineers. Thayer spent the great majority of the next 30 years as the chief engineer for the Boston area. During this time he oversaw the construction of both
Fort Warren and
Fort Independence to defend Boston Harbor. Thayer's great engineering ability can be observed in both of the above-mentioned forts. He was elected as a member of the
American Philosophical Society in 1838. Thayer was a member of the Board of Engineers for Coast Defenses, April 2, 1833, to December 21, 1857, and was President of the Board from Dec. 7, 1838. He temporarily commanded of the Corps of Engineers from December 21, 1857, to December 22, 1858, while its commander, Colonel
Joseph G. Totten, was on a leave of absence. In December 1858 Thayer was placed on an extended sick leave of absence. He did not play an active role in the American Civil War. In August 1861,
Fort Thayer, an earthwork fort part of the
Civil War Defenses of Washington, DC, was built and named in his honor. Thayer retired from the Army on June 1, 1863, with the rank of colonel in the Corps of Engineers. He was retired under the first act regulating the retirement of Army officers which required the retirement of any officer with more than 45 years of service. ==Death and legacy==