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Novel Cherenkov detector upgrades favour GEM and ThickGEM based MPGD systems. These detectors have reduced ion backflow, fast signal formation, high gain, and could suppress the MIP signals as well. Their common drawbacks are the inefficiencies of photo-electron collection fromthe top of the ThickGEM and the local variation of multiplication due to the special geometry. The developed high resolution scanner using focused UV light gave the possibility to study single photo-electron response of MPGDs in the sub-millimeter scale. Revealing the microstructure of photo-efficiency and local gain provides a new tool to quantitatively compare different ThickGEM geometries and field-configurations, and thus optimize the detector parameters. The presentation will focus on the key elements of the scanning system; and on the microstructure evolution of different ThickGEM configurations.