Nanometer-scale Ge islands and pits are self-organized during GeH4 vacuum-ultraviolet-excited chemical vapor deposition on a Ge(001) substrate. We carried out simulation and fitting on real-time ellipsometric ΨΔ trajectories that reflect undergoing changes in the surface morphology. The islanded Ge epitaxial layer was optically represented by multiple stacked slabs with linearly varying graded indices from the bottom to the top of the islands. The dielectric function of each slab was calculated by mixing the dielectric functions of Ge with that of voids under Bruggeman effective medium approximation. The only model that could reproduce the roughening ΨΔ trajectory was preferential nucleation of Ge on the top surface of truncated pyramidal islands after almost 100% of the initial surface had been wet. The smoothing section was consistent with the model assuming nucleation on the sidewalls of islands as well as on the top surface, which led to simultaneous deepening and narrowing of the valleys or pits between the islands. This smoothing model was supported by atomic force microscopy images.

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