This research focuses on measurements of a convective shear-layer instability seen naturally in quiet hypersonic flow. Experiments were carried out in the Boeing/AFOSR Mach 6 Quiet Tunnel (BAM6QT) at Purdue University. The BAM6QT provides low-disturbance hypersonic flow with freestream noise levels similar to what would be experienced by a flight vehicle. To obtain high-speed, off-the-surface measurements of the instability, a modified focused laser differential interferometer (FLDI) was first designed to work with the contoured Plexiglas windows available in the tunnel.<div><br>A cone-cylinder-flare geometry was then selected to study the instabilities related to an axisymmetric separation bubble at Mach 6. The sharp cone had a 5-degree half-angle, while flare angles of 10 degrees and 3.5 degrees were tested to compare axisymmetric compression with and without separation, respectively. Under quiet flow, laminar separation and reattachment was confirmed by schlieren and surface pressure-fluctuation measurements. Coherent traveling waves were observed. These were attributed to both the second-mode instability, as well as a shear-generated instability from the separation bubble. The symmetry of the bubble was found to be highly sensitive to angle of attack. Additionally, by introducing controlled disturbances on the cone upstream of the separation, larger-amplitude shear-generated waves were measured while the second-mode amplitudes remained unchanged. Therefore, the shear-generated waves were amplified moving through the shear layer, while the second mode remained neutrally stable. These appear to be the first measurements of traveling waves that are generated in the shear layer of a separation bubble in hypersonic flow. <br></div>