Isolator flows downstream of the scoop model inlet were visualized by using a planar laser Rayleigh scattering imaging technique. The scoop model was designed for a cruise Mach number of 6. The isolator flows were visualized for two contraction ratios of the scoop inlet (4 and 5) and various freestream Reynolds number conditions. Two freestream Mach numbers were tested to study the flows at the on-design (Mach number 6) and off-design (Mach number 4.5) conditions. Pseudo-cross-sectional flow structures of the isolator were constructed by using averaged planar images from multiple planar imaging planes. The flow visualization found that there exist curved shockwaves and localized flow separation, and three-dimensional shockwave–boundary layer interaction occurs locally affecting boundary layer growth. The visualization showed that Reynolds number determines the thickness of the boundary layer and the size of eddies. Similar overall flow and shockwave structures were observed for different freestream Mach number and Reynolds number conditions. Differences in shockwave angles, impinging shock location, the size of the core flow, and the size of the flow structure were discussed for various flow conditions.