Electron microscopy has proved to be a major tool to study the structure of self-assembled amphiphilic block copolymer particles. These specimens, like supramolecular biological structures, are problematic for electron microscopy because of their poor capacity to scatter electrons and their susceptibility to radiation damage and dehydration. Sub-50 nm core-shell spherical particles made up of poly(hydroxyethyl acrylate)-b-poly(styrene) are prepared via polymerization-induced self-assembly (PISA). For their morphological characterization, we discuss the advantages, limitations, and artefacts of TEM with or without staining, cryo-TEM, and SEM. A number of technical points are addressed such as precisely shaping of particle boundaries, resolving the particle shell, differentiating particle core and shell, and the effect of sample drying and staining. TEM without staining and cryo-TEM largely evaluate the core diameter. Negative staining TEM is more efficient than positive staining TEM to preserve native structure and to visualize the entire particle volume. However, no technique allows for a satisfactory imaging of both core and shell regions. The presence of long protruding chains is manifested by patched structure in cryo-TEM and a significant edge effect in SEM. This manuscript provides a basis for polymer chemists to develop their own specimen preparations and to tackle the interpretation of challenging systems.