Captain Pratt started a prison school for the men. When the prisoners were allowed to return home in 1878, he convinced 22 of them to continue their schooling. Several of them were accepted at The Hampton Institute, a school for freed slaves in Virginia. He resigned his Army commission upon the opening of Carlisle to practice his ideas about educating Indians.
Pratt's goal was to "kill the Indian, not the man."[2.ibid] At the time, reformers believed that assimilation and off-reservation boarding schools were a better policy than extermination, although extermination had been the primary policy to date. Extermination included shooting to kill, starving to death and some believed deliberately infecting Indians with European diseases and/or withholding vaccine for smallpox. In other words, a deliberate policy of Indian Genocide. The native population in the Americas has been estimated at ninety to one hundred million prior to the arrival of Europeans. The American Indian population in North America has been estimated at 12 million in the fifteen hundreds and by the early 1900s the American Indian population had been reduced to about 475,000.
Boarding schools became a part of official Government Indian policy after Carlisle opened. Most were run by church organizations, but they all followed the same mind-control model established by Pratt and attendance was mandatory. Even today, Tony Hillerman in his novel, The Shape Shifter, 2006, has Lt. Joe Leaphorn, Retired, of the Navajo Tribal Police mention that Navajo children were shipped off the reservation to Boarding schools. . Boarding school mind-control techniques included the following: 1]Many boarding schools were established far away from reservations so that students would have no contact with their family or friends. Parents were discouraged from visiting and, in most cases, students were not allowed to go home during the summer. 2] Indian boarding school students wore military uniforms and were forced to march. 3] They were given many rules and no choices. To disobey meant swift and harsh punishment. 4.] Students were forbidden to speak their language. 5] They were forbidden to practice their religion and were forced to memorize Bible verses and the Lord's Prayer. 6] Their days were filled with so many tasks that they had little time to think. 7] Indian students had no privacy. 8] Boarding school students were expected to spy on one another and were pitted against each other by administrators and teachers. 9] Students were taught that the Indian way of life was savage and inferior to the white way. They were taught that they were being civilized or "raised up" to a better way of life. 10] Indian students were told that Indian people who retained their culture were stupid, dirty, and backwards. Those who most quickly assimilated were called "good Indians". Those who didn't were called "bad" Indians. 11]The main part of their education focused on learning manual skills such as cooking and cleaning for the girls and milking cows and carpentry for the boys. In my opinion, this wasn't much different from the public schools which in the 1940s were teaching Home Economics to the 7th and 8th grade girls and printing, woodworking, metalworking and mechanical drawing to the boys. 12] Students were shamed and humiliated for showing homesickness for their families. 13] When they finally did go home, as to be expected, many boarding school students had a difficult time fitting in.
By the 1930s most off-reservation boarding schools were closed, but many American Indian children who lived on reservations still attended boarding schools located there. Missionaries ran some of these schools and the Bureau of Indian Affairs ran others. More than a few of them still retained an authoritarian structure and the goal of "civilizing" students.
In all, more than 100,000 Indian children attended 500 boarding schools that were established after the Carlisle model. "It is a testimony to the strength, courage and persistence of Indian People that the people and their diverse cultures survived this prolonged attack."
, ,  American Indian Boarding Schools-Brainwashing and Boarding Schools:Undoing the Shameful Legacy: http://www.kporterfield.com/aicttw/articles/boardingschool.html
 Tony Hillerman, "The Shape Shifter", Chapter 16, HarperCollins Publishers 
 O. Ned Eddins, "Plains Indian Smallpox":http://www.thefurtrapper.com/indian_smallpox.htm