Intestinal Transplant Procedure. In an Intestinal transplant, the small intestine (small bowel) is surgically removed (along with any other diseased organs such as the liver), and replaced with healthy organ(s).ntestinal Transplant Procedure. In an Intestinal transplant, the small intestine (small bowel) is surgically removed (along with any other diseased organs such as the liver), and replaced with healthy organ(s).