Energy-filtered transmission electron microscopy provides an opportunity to map the nanoscale elemental composition in polymeric systems. Nevertheless, it presents its own set of unique challenges in its application to soft materials. Here, we outline an optimized protocol for elemental mapping in soft materials using sulfur mapping of polymer/fullerene mixtures as an example. Three factors are crucial: (1) focusing at zero-loss, (2) using an objective aperture, and (3) maximizing signal-to-noise and counts for the chosen imaging conditions. Analyzing the corresponding source images, bright field images, and thickness maps can ensure optimum conditions are achieved for elemental mapping of polymers.