The electronic and optical properties of transparent conducting oxides (TCOs) are closely linked to their crystallographic structure on a macroscopic (grain sizes) and microscopic (bond structure) level. With the increasing drive towards using reduced film thicknesses in devices and growing interest in amorphous TCOs such as n-type InGaZnO 4 (IGZO), ZnSnO 3 (ZTO), p-type Cu x CrO 2 , or ZnRh 2 O 4 , the task of gaining in-depth knowledge on their crystal structure by conventional X-ray diffraction-based measurements are becoming increasingly difficult. We demonstrate the use of a focal shift based background subtraction technique for Raman spectroscopy specifically developed for the case of transparent thin films on amorphous substrates. Using this technique we demonstrate, for a variety of TCOs CuO, a-ZTO, ZnO:Al), how changes in local vibrational modes reflect changes in the composition of the TCO and consequently their electronic properties.