Variable stars, such as Classical Cepheids, have been used for over one hundred years as probes for determining astronomical distances; these distances can be used to map out the three-dimensional (3D) structure of nearby galaxies. Exploiting the effect that moving to the mid-infrared has on Cepheid magnitudes and light curves, we can now map our nearest galaxies in 3D at fidelities never before achievable. Combining data from the OGLE-IV catalogue with mid-infrared photometry from the Spitzer Space Telescope, ~5000 fundamental mode Cepheids are being used to trace the 3D structure of the Magellanic Clouds, two dwarf galaxies in orbit around the Milky Way. An automated photometry pipeline has been developed to obtain precise mean magnitudes and light curves for Cepheids in the Magellanic System. These mean magnitudes are used to produce a mid-infrared period-luminosity (PL) relation, with the zero point calibrated using Gaia parallaxes of Cepheids. As a result, we can produce distance measurements accurate to 5% for individual Cepheids. These detailed maps are being used to probe the geometric and chemical structure of the Magellanic Clouds as well as their interaction and dynamical histories. Future inclusion of RR Lyrae stars will allow us to also trace the old stellar population of the system. With the increased precision expected from future Gaia data releases, this project will combine Gaia’s astrometric solution with our precise 3D position measurements to further constrain the past trajectories of these galaxies.