We present recent studies using the near-infrared instrument AMBER of the VLT Interferometer (VLTI) to investigate the structure and shaping processes within the extended atmosphere of AGB stars. Spectrally resolved near-infrared AMBER observations of the Mira variable S Ori have revealed wavelength-dependent apparent angular sizes. These data were successfully compared to dynamic model atmospheres, which predict wavelength-dependent radii because of geometrically extended molecular layers. Most recently, AMBER closure phase measurements of several AGB stars have also revealed wavelength-dependent deviations from 0/180 deg., indicating deviations from point symmetry. The variation of closure phase with wavelength indicates a complex non-spherical stratification of the extended atmosphere, and may reveal whether observed asymmetries are located near the photosphere or in the outer molecular layers. Concurrent observations of SiO masers located within the extended molecular layers provide us with additional information on the morphology, conditions, and kinematics of this shell. These observations promise to provide us with new important insights into the shaping processes at work during the AGB phase. With improved imaging capabilities at the VLTI, we expect to extend the successful story of imaging studies of planetary nebulae to the photosphere and extended outer atmosphere of AGB stars.