After completing multi-engine flight training in November 1946, Allen was assigned to Strategic Air Command's 7th Bombardment Group at Carswell Air Force Base, Texas, where he flew B-29 Superfortress bombers, and then the new and very long-range Convair B-36 bomber. Allen also served in various technical positions in the area of nuclear weapons. Allen also attended the Air Tactical Course at Tyndall Air Force Base, Florida, and next he returned to Carswell Air Force Base as a flight instructor and as an assistant Special Weapons Officer for the 7th Bombardment Wing.