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The spatially precise integration of arrays of micro-patterned two-dimensional (2D) crystals onto three-dimensionally structured Si/SiO$_2$ substrates represents an attractive strategy towards the low-cost system-on-chip integration of extended functions in silicon microelectronics. However, the reliable integration of the arrays of 2D materials on non-flat surfaces has thus far proved extremely challenging due to their poor adhesion to underlying substrates as ruled by weak van der Waals interactions. Here we report on a novel fabrication method based on nano-subsidence which enables the precise and reliable integration of the micro-patterned 2D materials/silicon photodiode arrays exhibiting high uniformity. Our devices display peak sensitivity as high as 0.35 A/W and external quantum efficiency (EQE) of ca. 90%, outperforming most commercial photodiodes. The nano-subsidence technique opens a viable path to on-chip integrate 2D crystals onto silicon for beyond-silicon microelectronics.