Stuart Macrae's career in engineering began when he briefly worked for the Westinghouse Brake and Saxby Signal Company as an apprentice. He then became a trainee draughtsman at an aircraft company, soon moving on to design work, including a project for the Air Ministry at the end of the First World War designing bomb release gear. After the war, Macrae returned to aircraft design work, then became a technical journalist, eventually becoming editor of a number of technical journals. While Macrae was working for Odhams Press Limited in 1939 as editor of the magazine Armchair Science, he was recruited by Major Millis Jefferis to be his second-in-command in the Military Intelligence Research (MIR) branch of the War Office.

MIR was responsible for inventing many sabotage devices for organisations including the Special Operations Executive (SOE). Later in the war it turned to the development of high explosives, including weapons which Macrae worked on such as the anti-tank grenade, or Sticky Bomb, the magnetic Limpet Bomb, the "M" anti-personnel mine, the Water Bomb, and numerous other bombs and grenades.

When SOE was formed in 1940 from MIR and other organisations, Jefferis's technical group became a department of the Ministry of Defence instead, known as M.D.1, which was based at Whitchurch, Buckinghamshire. Macrae was responsible for the management of M.D.1, but in November 1945 the department was merged with the Armament Development Establishment, and was closed down in early 1947.