The Stratospheric Observatory for Infrared Astronomy (SOFIA) is a Cassegrain telescope with a 2.7m primary mirror flying at altitudes up to 45 kft. One particular challenging aspect of an airborne observatory is the pointing control and image stability. The main control system consists of three cascaded SISO attitude and rate loops. The Fine Drive (FD) as the main actuator can move the telescope in all three axes by + / - 3°. Its bandwidth is currently limited to 3-5 Hz (depending on the axis), which prevents it from compensating higher frequency eigenmodes and especially modes in between 5-10 Hz. The compensation of these modes and of higher frequency excitation is currently achieved with a feed-forward loop to the active secondary mirror. A faster main actuator (the Fine Drive) could better counteract low frequency disturbances and would reduce the load on the secondary mirror. Flexible modes above 10 Hz are the main task of the Flexible Body Compensation system and not part of the FD scope. As the eigenfrequencies nonetheless occur on the gyro sensor measurements in the FD loop, the controller gains are conservatively chosen to not amplify these modes. This paper discusses first the derivation of a very accurate telescope plant model for simulation and then a specifically designed observer which minimizes the impact of the telescope resonance frequencies on the FD feedback. The flexible modes are part of the observer noise model. It is shown that this observer can stabilize the closed loop system and minimize the necessity of compensation filters, thereby enabling a faster FD controller.