Measurement and control is an important step for production-worthy through silicon vias etch. We demonstrate the use and enhancement of an existing wafer metrology tool, spectral reflectometer by implementing novel theoretical model and measurement algorithm for high density through-silicon via (HDTSV) inspection. It is capable of measuring depth and depth variations of array vias by Discrete Fourier Transform (DFT) analysis in one shot measurement. Surface roughness of via bottom can also be extracted by scattering model fitting. Our non-destructive solution can measure TSV profile diameters as small as 5 μm and aspect ratios greater than 13:1. The measurement precision is in the range of 0.02 μm. Metrology results from actual 3D interconnect processing wafers are presented.