The problem of resonance energy transfer in planar and bilayer geometries with heterogeneous chromophore distributions is studied. Donor fluorescence decays were obtained using the Monte Carlo method for lateral phase separation into continuous and domain phases, and also for probe segregation in linear defects. The generated synthetic curves were analyzed with the mean local concentration model (Liu et al. Chem. Phys. 1993, 177, 579). It is shown that a significant number of heterogeneity cases can be adequately described by a sum of two Gaussians acceptor concentration distribution. The ability of the analysis method to recover correct acceptor concentration distributions was also tested in more critical conditions, i.e., after convolution of synthetic decay curves and addition of Poisson noise, to emulate experimental fluorescence decay curves. The analysis methodology is shown to be useful to describe probe heterogeneity caused by phase separation, and important parameters (such as the probe partition coefficients) can be recovered.