The use of the focused ion beam (FIB) technique for cross-sectional transmission electron microscopy (TEM) specimen preparation of polymer solar cells deposited on glass substrates is described. Ultra-thin sections were prepared using the 'lift-out' technique. Electron microscopy investigations of these specimen resulted in detailed morphological information of the devices (e.g. thickness and interface roughness of the layers). In comparison with standard sample preparation routes for TEM investigations the used technique is well suited for precise sectioning of hybrid structures.