This work is concerned with the study of Nafion ionomer incorporation in model nanoporous structures with well-defined pore structure and size. A key challenge is quantification of the distribution of ionomer in these nanoporous structures. The thickness of ionomer films is anticipated to be a few nanometers, which limits the experimental observation to x-ray and electron microscopy based techniques both of which are known to damage polymers and also limit size of investigated volume of few tens of nanometers cubed. In this work, we have adopted laser scanning confocal fluorescence microscopy (LSCFM). The ionomer is first tagged with a fluophor. The tagged ionomer in dispersion diffuses through the pores of the nanoporous inorganic membranes of few tens of microns in thickness. The distribution of ionomer in the nanoporous membrane is mapped by LSCFM as function of pore size, ionomer concentration and exposure time. The figure below shows an example of Nafion ionomer distribution in anodized aluminum oxide nanoporous membrane.The results are cross-correlated with energy dispersive x-ray (EDX) characterization of selected samples. One of the peripheral questions, we wish to answer is whether Nafion ionomer can diffuse through sub-10 nm size pores that may exist in the secondary pores formed by aggregation of 30 nm Pt/C nanoparticle catalysts used for conventional catalyst layers of PEFCs. Furthermore, the methodology offers an attractive option for mapping long-range distribution of ionomer in tens of micron thick catalyst layers.