Thick segmented scintillators, incorporating a 2-dimensional matrix of optically-isolated scintillator elements, have shown considerable potential for improving the performance of megavoltage active matrix, flat-panel imagers (MV AMFPIs). While over a factor of 20 improvement in DQE at zero spatial-frequency has been demonstrated for prototypes incorporating CsI(Tl) and BGO scintillators, less-than-optimal element-to-element alignment (misalignment) as well as mis-registration to the underlying AMFPI array pixels can result in spatial resolution loss, reducing DQE improvement at higher spatial frequencies. In this presentation, a method to restore spatial resolution and DQE, based on the use of a high resolution AMFPI array along with special binning techniques, is investigated. The effect of misalignment and mis-registration of segmented scintillators on imaging performance was investigated theoretically and empirically through determination of the modulation transfer function (MTF) and DQE, as well as through realization of reconstructed images of a phantom in a cone-beam CT geometry. The empirical investigation, which was conducted using a 6 MV photon beam, employed a prototype BGO segmented scintillator consisting of 120×60 elements separated by 50 μm-thick septal walls and an element-to-element pitch of 1016 μm. The scintillator was coupled to a higher resolution 127-μm-pitch AMFPI array. Misalignment and mis-registration result in significant degradation of spatial resolution, leading to DQE reduction at non-zero spatial frequencies. While mis-registration for a well-aligned scintillator can be overcome through 8×8 binning of the array pixels to match the scintillator elements, any misalignment will affect such binning and lead to spatial resolution loss. However, the use of 'selective' binning, consisting of the selection of those pixels corresponding to the interior locations of each element, improves resolution while preserving DQE. The use of high-resolution AMFPI arrays combined with selective binning allows prototype AMFPIs incorporating thick, segmented scintillators to achieve imager performance limited only by scintillator performance. Work Supported by NIH grant R01-CA051397.