Muir joined the Royal Air Force at the outbreak of the Second World War, and spent several years in the photographic technical school taking slow motion film of parachute jumps on a project intended to decrease the frequency of parachutes failing (sometimes called a ‘Roman Candle’). His work provided the manufacturers with the information they needed to improve both the equipment and the training, which was very effective in reducing the number of failures as well as the fatality and injury rate. He was also assigned to take pictures of the agents of the Special Operations Executive (SOE) for identity documents at the training centre at RAF Ringway.
Muir, as a photographic technician, was posted to Iceland, which was then a Danish possession under British occupation, and while there, he did some work for the forces radio station. Also while stationed in Iceland – as he described in his memoirs A Kentish Lad – Muir suffered a medical condition which required the surgical removal of one testicle.