The exposure of thick UV sensitive polymer layers leads to the formation of self-organized refractive index filaments, which appear after a certain layer thickness, typically in the range of 50 μm. This effect has strong influence on the fabrication of, e.g., high precision micro-optical elements. In particular, diffraction limited micro-lenses with high sag or high aspect ratio on-chip collimators require a perfect index homogeneity. We show that the saturable and irreversible change of the polymer refractive index causes a modulational instability (MI), which finally leads to the creation of filaments. It will be presented that a maximum growth rate for a certain spatial frequency of an initial perturbation exists. This MI gain determines the dynamics of the filament formation. The impact of the exposure conditions, e.g., chemical process parameters, on the homogeneity of the UV cured polymer is discussed for ORMOCERTM type polymers.