Born in Seneca Falls, New York on January 26, 1829, Marshall graduated from West Point in 1850. He served in the Utah War as a First Lieutenant. He also fought in the Battle of the Colorado River in 1859 during the Mohave War in Arizona. He was promoted to Captain in May 1861, and became a Colonel of volunteers in April 1862. He was seriously wounded while leading the 13th New York Volunteers in the Battle of Fredericksburg, and did not return to active duty until early 1864. He was captured in the Battle of the Crater, and was held as a prisoner of war until April, 1865.