Atomic number contrast scanning transmission electron microscopy (Z-STEM), with atomic resolution and sub-nanometer resolution scanning transmission electron microscope electron energy loss spectroscopy (STEM-EELS), was used to study single colloidal CdSe semiconductor nanocrystals embedded in MEH-PPV polymer films. The atomic column-resolved Z-STEM image provides information both on the lateral shape of the nanocrystal, as well as the relative thickness of the individual atom columns from a single image. The three-dimensional shape profile reconstructed from the data matches the predicted model. Furthermore, the sublattice is resolved so the polar surfaces can be uniquely identified. Sub-nanometer resolution EELS measurements on an individual nanocrystal indicate the presence of oxygen. The spatial distribution of the oxygen signal in the EELS measurement suggests a thin oxide layer on the nanocrystal surface.