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Rigorous coupled wave analysis (RCWA) is conducted on in situ spectroscopic ellipsometry data to understand profile evolution during film deposition inside nanotrenches. Lithographically patterned SiO 2 nanotrenches are used as test structures. The nanotrenches are 170 nm wide at the top with a taper angle of 4.5° and are 300 nm in depth. Atomic layer deposition of ZnO is used as a model process where the thickness (cycles) of the film is varied from 0 (0 cycles) to 46 nm (300 cycles). The analysis predicts transient behavior in deposition affecting film conformality and changes to the trench taper angle. In the process, the aspect ratio varies from 2.05 at the start of the process to 6.67 at the end. The model predicts changes in the refractive index of the ZnO film as a function of thickness. The real and imaginary parts of the refractive index at a wavelength of 350 nm change from 1.81 to 2.37 and 0.25 to 0.87, respectively. Scanning electron microscopy cross sections confirm thickness at the top and bottom of the trench to within 13% of those predicted by RCWA. The experimentally measured conformality degrades as film deposition proceeds from 97.3% at 100 cycles to 91.1% at 300 cycles. These results demonstrate the potential of using RCWA for continuous and in situ monitoring of growth inside 3D nanostructures.