Following the great success of traditional microfluidic devices across many disciplines, a new class of microfluidic systems emerged in recent years, which features finely tuned, localized surface modifications within the microstructures in order to keep up with the demand for devices of ever increasing complexity (lab on chip, assay on chip, etc.). Graft photopolymerization has become a powerful tool for such localized surface modifications particularly in combination with poly(dimethylsiloxane) (PDMS) devices, as it is compatible with many functional monomers and allows for high spatial resolution. However, application within enclosed PDMS microstructures and in particular well-controlled surface-directed polymerization remains challenging. Detailed understanding of the interaction between photoinitiator, benzophenone (BP), and polymer matrix is needed. We have developed a visualization technique, which allows for observation of reacted BP in situ within the PDMS matrix. We present a detailed study on solvent-driven BP diffusion providing results essential to successful surface treatment. We also identified and investigated photoinitiator inhibition by oxygen and provide appropriate mitigation strategies.