As advanced packaging evolves with 2.5D/3D integration, the demand grows for the inspection of subsurface nanostructures and defects within silicon (Si), ensuring reliability and yield in modern electronics. In this paper, we demonstrate coherent Fourier scatterometry (CFS) at a near-infrared wavelength (λ=1055 nm) for noninvasive inspection of nanostructures buried within Si. Despite Si's transparency in this spectral range, its high refractive index causes strong Fresnel reflections at the air–Si interface. To eliminate these unwanted signals, we employ two distinct approaches: (i) a split detector to subtract reflections in defect inspection mode, and (ii) a reduced coherence length, below lasing threshold, combined with spatial filtering, for retrieving far-field diffraction patterns in grating inspection mode. We systematically investigate how thickness of overlying Si (without overlying Si wafer, with 300 μm thick Si wafer, and with 500 μm thick Si wafer) affects scattering signals of the buried nanostructures. We demonstrate the detection of low contrast polystyrene nanospheres (down to 400 nm, well below the diffraction limit of λ/(2NA)≈959 nm) buried under 500 μm of Si. Further, we successfully detect nanopillars ≥100 nm and nanopits ≥225 nm. We also analyze the influence of spherical aberrations, which increases linearly with the thickness of the Si layer, resulting in a degradation of the focal spot quality. Beyond isolated defects, we retrieve the diffraction patterns of a 1430 nm period grating under 500 μm of Si, with minimal distortion relative to when no Si layer is present. Overall, these results highlight CFS as a robust, high-sensitivity technique for in-depth inspection in microelectronics and photonic applications, demonstrating potential for failure analysis, process control, and metrology in advanced packaging environments.