2D thermospheric wind fields, at both E- and F-region altitudes within a common vertical volume, were made using a Scanning Doppler Imager (SDI) at Poker Flat, Alaska, during a substorm event. Coinciding with these observations were F-region plasma velocity measurements from the Super Dual Auroral Radar Network (SuperDARN), and estimations of the total downward and upward field-aligned current density from the Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE). This combination of instruments gives an excellent opportunity to examine the spatial characteristics of high latitude ionosphere-thermosphere coupling, and how a process which is triggered in the magnetosphere (the substorm) affects that coupling at different altitudes. We find that during the substorm growth phase, the F-region thermospheric winds respond readily to an expanding ionospheric plasma convection pattern, whilst the E-region winds appear to take a much longer period of time. The differing response timescales of the E- and F-region winds is likely due to differences in neutral density at those altitudes, resulting in E-region neutrals being much more ‘sluggish’ with regards to ion-drag. We also observe increases in the F-region neutral temperature, associated with neutral winds accelerating during both substorm growth and recovery phases.