One of the most dramatic meteorological perturbations in the middle atmosphere is the sudden stratospheric warming (SSW). This usually occurs at least once per Northern winter and results in large (up to 50K) temperature increases, wind reversals and hemispheric transport perturbations. It is now understood that the effects of SSWs resonate up to much higher altitudes, including the mesosphere (up to 90 km) and possibly even the thermosphere (above 90 km). However the actual manifestation of these SSWs on the mesospheric and lower thermospheric temperature structure remains uncertain, with different models yielding different answers, probably related to the treatment of gravity waves. We examine this question with the Navy's operational forecast system which has been extended up to the lower thermosphere. This model, NOGAPS-ALPHA (Advanced Level Physics High Altitude) has been used to perform several case studies of different SSW events over the last several years. The results will be compared with observations from two NASA satellites, TIMED and AURA, both of which are measuring the temperature from the stratosphere to the lower thermosphere. Preliminary comparisons confirm the existence of a perturbed layer in the thermosphere; however, the altitude at which this occurs appears lower than initially predicted.