The exposure of UV-sensitive polymers leads to a saturable and irreversible change of the refractive index up to 0.1 due to the polymerization generated changing material density. This non-linear phenomenon has a strong impact on the structure formation in the UV-assisted fabrication of thick micro-optical elements. E.g., appearing self-focusing effects and time-dependent absorption influence the sidewall geometry, while self-guiding effects have impact on the internal index distribution. Based on a material model, which describes the index change as a function of a set of process parameters, a modified iterative beam propagation algorithm is developed to simulate the structure formation. It is shown theoretically as well as experimentally that the variation of process parameters, e.g. the photo initiator concentration or the initial complex exposure field distribution, offer possibilities to control the structure formation and to make use of the self-organizing tendency. The developed patterning method is optimized for standard contact lithography processes, e.g., in a mask aligner, requiring only low exposure intensities below 10 mW/cm². This enables for performing integral wafer-scale patterning processes, e.g., on optoelectronical substrates. The realization of arrayed on-chip conic light concentrators are presented as an exemplary application.