After a year in Marietta, Canty received a letter from Booker T. Washington requesting that he write to James Edwin Campbell, principal of the West Virginia Colored Institute in Farm, West Virginia (present-day Institute, West Virginia). Campbell had written Washington seeking a Tuskegee graduate to serve as superintendent of mechanics at the institute, and Washington recommended Canty for the position. Canty accepted and began his duties as the superintendent of mechanics at the institute on January 3, 1893. He was the third teacher to join the institute’s faculty. West Virginia Colored Institute had been founded in 1891 under the Morrill Act of 1890, to provide West Virginia’s African Americans with education in agricultural and mechanical studies.

From his arrival in 1893 until the fall of 1898, Canty carried out the school’s industrial work and education without assistance. As superintendent of mechanical industries, he taught blacksmithing, carpentry, and mechanical drawing. In addition to teaching, Canty was in charge of campus maintenance and installed the institute’s sewerage system and heating systems in its buildings. In his first year, Canty established a drill team at the institute because “he felt that the boys needed discipline”. Canty only had one rifle for the drill team, so he made the students carve their own wooden rifles. In 1894, Canty also taught in the institute’s literary department.

In the early summer of 1898, the institute’s principal John H. Hill resigned to accept a commission as a first lieutenant in the United States Volunteers. Following Hill’s resignation, the institute’s Board of Regents named Canty as the acting principal. While acting principal, Canty established the institute’s first military training corps for students, which emphasized physical fitness and sports as major parts of its program. Following the onset of the Spanish–American War, the state appropriated funds for uniforms and Krag–Jørgensen rifles for the training corps. The training corps later became the school’s Reserve Officers’ Training Corps (ROTC) unit. Canty served as acting principal until the board’s selection of James McHenry Jones as principal on September 21, 1898.

Canty’s department of mechanical industries was located in the institute’s Machinery Hall. It was expanded in 1903 and rededicated in 1904 as the A. B. White Trades Building, named for West Virginia Governor Albert B. White. The trades building expansion cost $35,000 to complete. Canty planned and supervised the building’s construction.

By 1905, Canty’s work at the institute consisted of superintending the school’s mechanical industries and teaching mechanical drawing. Canty was one of three instructors when he arrived at the institute in 1893 and the school had 30 students, and by 1905, the institute had grown to 18 teachers and 187 students. In that time, Canty’s department had grown to include instruction in: blacksmithing, carpentry, masonry, mechanical drawing, plastering, printing, and wheelwrighting. Canty was the only instructor in the mechanical industries department when he arrived in 1893; by 1906, his department had ten employees, seven of whom were under his supervision. Canty was credited with building up the institute’s mechanical industries program.

In 1907, Canty organized and helped set up the West Virginia Colored Institute’s industrial and student display and the West Virginia exhibit at the Jamestown Exposition in Norfolk, Virginia. Canty resigned as superintendent of mechanical industries at West Virginia Colored Institute in 1914. Albert C. Spurlock succeeded him in this position. Canty continued to serve on the institute’s faculty until his retirement in 1948. That year, Canty arranged for the construction of West Virginia State College’s military training corps rifle range.