Topography measurement of high aspect ratio trench array using coherence scanning interferometry presents significant challenges because the numerical aperture of detection light is constrained by the trenches. Altering the detection light to penetrate the sample like near-infrared light for silicon could overcome this obstacle, but the trench array spreads the detection light. This study introduces a coherence scanning interferometry model based on three-dimensional point spread function and assuming sample is transparent to detection light, which is realized by integrating rigorous numerical electromagnetic field solution to quantify the modulation aberrations of detection light by transparent trench arrays, and theoretical angular spectrum diffraction utilized for far-field interference imaging. This model facilitates a thorough analysis of the aberrations introduced by trench arrays, encompassing comparisons between trench arrays and a single trench, as well as between the symmetric region of the array and the asymmetric region at the edge. Additionally, an investigation into the impact of unified compensation for low-order aberrations on the topography reconstruction is presented, and we find the sample-induced aberration compensation method utilizing a deformable mirror that we previously proposed for a single trench is still effective confronting trench array. Experimental measurements are performed on silicon trench arrays with the aspect ratio of up to 20:1 and the period of approximately 10 µm to validate the effectiveness of our model and measurement methods, thus providing valuable insights for enhancing high aspect ratio manufacturing.