The microlens array (MLA) with a small geometric footprint and unique performances, is the key enabler to push the development of photonic devices toward miniaturization, multi-function and large-scale integration. However, the realization of 100% fill-factor (FF) MLAs with high controllability and its mass manufacturing without complex steps has always been a difficult issue. Here, we propose an efficient, highly flexible and low-cost manufacturing approach for MLAs with a high FF via snapshot polarization patterning. The digitalized linear polarization pattern was distributed across the photo-alignment layer with both high efficiency and accuracy, enabling large-area liquid crystal MLA with parameter controllability from element to element. The MLA manufacturing process does not involve developing, etching and deposition steps and is suitable for industry up-scaling. We further proposed a novel compact compound-eye imaging system for biometrics with the obtained MLAs. The 100% FF MLA enables high light utilization efficiency and low background crosstalk, yielding compact biometrics indentation with high recognition accuracy. The realization of such planar optics would lead to a plethora of different miniaturized multiaperture imaging systems in the future.