We are investigating membrane-based sorting processes in polarized epithelial MDCK cells, which most likely involves membrane microdomains. We have postulated that proteins contained in these microdomains, cluster, and to prove this, we have internalized differently fluorophore labeled pIgA-R ligands in MDCK cells, stably transfected with polymeric IgA receptors (pIgA-R), from opposite plasma membranes. Our previous work showed that these receptor-ligand complexes colocalize in the apical recycling endosome (ARE), underneath the apical plasma membrane. Quantitative one-photon confocal and 2-photon (2-P) FRET microscopy allowed us to calculate energy transfer efficiency (E%). Unquenched donor levels where established based on a novel algorithm, which corrects the FRET contamination of acceptor bleed-through and donor crosstalk. Using different emission filters also confirmed the veracity of the algorithm. 2-P FRET allows the selection of a specific donor wavelength, which does not precipitate acceptor bleed-through, a clear advantage over 1-P confocal microscopy. Results show that E% is independent of acceptor levels, an indication of a clustered distribution, as in random distribution E% rises with increasing acceptor levels. However, E% decreases with increasing donor and donor:acceptor ratio levels, which we have termed 'donor geometric exclusion', where some donors in a cluster block others from interacting with an acceptor. We submit that this is a second indicator for a clustered pattern, because in a random, dispersed situation donors are not likely to be in close proximity to have such an effect. We have developed a model explaining this phenomenon.