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Quantum fluctuations give rise to Casimir forces between two parallel conducting plates, the magnitude of which increases monotonically as the separation decreases. By introducing nanoscale gratings to the surfaces, recent advances have opened opportunities for controlling the Casimir force in complex geometries. Here, we measure the Casimir force between two rectangular gratings in regimes not accessible before. Using an on-chip detection platform, we achieve accurate alignment between the two gratings so that they interpenetrate as the separation is reduced. Just before interpenetration occurs, the measured Casimir force is found to have a geometry dependence that is much stronger than previous experiments, with deviations from the proximity force approximation reaching a factor of ~500. After the gratings interpenetrate each other, the Casimir force becomes non-zero and independent of displacement. This work shows that the presence of gratings can strongly modify the Casimir force to control the interaction between nanomechanical components., Comment: 31 pages, 7 figures