From May to June, 1863, Miller was assigned to the garrison at Fort Washington, Maryland.[1] He served as mustering officer for recruits in Baltimore, Maryland from June to August 1863, after which he returned to the garrison at Fort Washington, where he remained until March 1864.[1] From March to November 1864, Miller served on an examining board for new officers at the War Department headquarters in Washington, D.C., and Annapolis, Maryland.[1] He was promoted to captain on March 11, 1864.[1]
Miller returned to Washington, D.C., with his regiment at the end of the war.[1] He was promoted to brevet major on March 13, 1865, in recognition of his meritorious service during the campaign from Winchester to Richmond, Virginia.[1] He was promoted to brevet lieutenant colonel on March 31, 1865, in recognition of his gallant conduct at Dinwiddie Court House.[1]
Post-war
After the Civil War, Miller served with his regiment in Washington, D.C., from June 1865 to November 1867.[1] He was on duty at Fort McHenry, Maryland, from November 1867 to March 1870.[1] He was on duty in Charleston, West Virginia, from March to November 1870. From November 1870 to November 1872 Miller was again on duty at Fort McHenry.[1]
From September 1884 to November 1886, Miller was assigned to Fort Hamilton, New York, including a leave of absence for illness from June to October 1885.[1] From November 1886 to June 1888, Miller was inspector of rifle practice and acting ordnance officer for the Military Division of the Atlantic.[1] He was commander of the post at Fort Columbus, New York from July to December 1888.[1] From January 1889 to October 1894, Miller was again assigned to the staff of the Artillery School, this time as superintendent of instruction for Field Engineering, Electricity, Mechanical Engineering, and the Art of War.[1]
From November to December 1898, Miller commanded the Independent Division of the Eighth Army Corps while en route to the Philippines.[1] Upon arrival, he took part in the Philippine–American War as commander of the 1st Separate Brigade of the Eighth Army Corps.[1] The brigade was immediately ordered to take control of the city of Iloilo on the island of Panay from Spanish troops who were departing after the end of the Spanish–American War.[1]
Filipino insurgents occupied Iloilo after the Spanish departed but before Miller's command arrived.[1] the brigade took over most of the city in February 1899.[1] During this command, Miller passed an information copy of the memo describing the U.S. benevolent assimilation policy for the Philippines to local officials styling themselves as the Federal Government of the Visayas.[4] Miller was unaware that General Elwell Otis had supplied a bowlderized version of the memo to Filipino leader Emilio Aguinaldo in Manila.[4] The unaltered version eventually made its way to Aguinaldo, who compared it to the altered one.[4] The contrast between the two versions made Otis appear to be deceptive, which increased tension between the U.S. occupation government and the Filipinos.[4]
On February 12, the 1st Separate Brigade captured the city's district of Jaro, then successfully defended against three insurgent counterattacks.[1] In February 1899, Miller was promoted to brigadier general in the regular army.[1] In addition to commanding the 1st Separate Brigade, Miller commanded the Military District of Panay, Negros, Cebu, and Leyte.[1] He remained in these posts until reaching the mandatory retirement age of 64 on March 27, 1899.[1]
On November 5, 1863, Miller married Katherine Sprague Haskin (1843–1925), the daughter of General Joseph A. Haskin and sister of General William L. Haskin.[5] They were the parents of five children – Rebecca, Marcus, Mary, Lawrence, and Anne.[5] Rebecca Miller resided in Washington, D.C., and was active in civic and legacy organizations, including the National Society of the Colonial Dames of America, Daughters of the American Revolution, and Daughters of the United States Army.[7] Marcus Lyon Miller was a career officer in the United States Navy and attained the rank of captain.[5] Mary Appleton Miller was the wife of General Colden Ruggles.[5] Lawrence was a career Army officer and retired as a colonel.[5] Anne was the wife of Colonel Morris Keene Barroll.[5]
Legacy
Commemorative plaques marking unit locations during the Battle of Antietam include one for Miller and Battery G, 4th Artillery Regiment.[8] The plaque is located on what is now the east side of Branch Avenue in Sharpsburg, Maryland.[8]
Battery Marcus Miller was named for Miller in 1907.[9] One of several Coast Artillery gun emplacements intended to protect San Francisco Bay, the battery was located near what is now the southwest end of the Golden Gate Bridge.[9] Battery Marcus Miller remained in operation until it was dismantled in 1920.[9]
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