New drug-encapsulating particles were investigated using bright field (BF) scanning transmission electron microscopy (STEM) in a field emission gun (FEG) scanning electron microscope (SEM). Thickness characterization was done based on measuring the effective cross-section for interaction in our sample-detector configuration using calibration particles. A simplified analytical model, taking account of BF-STEM contrast and effective cross-section for interaction, was utilized for transforming projected two-dimensional BF-STEM images into three-dimensional thickness images. The three-dimensional characterization is demonstrated on a new family of biological materials composed of submicron to micron drug-free and drug-encapsulating particles. The importance of using BF-STEM in SEM, relative to other electron microscopy methods, is discussed as well as the lateral and depth resolution.