Thin-film samples of yttria-stabilized zirconia (YSZ), nickel oxide (NiO)-YSZ, and YSZ/nickel (Ni)-YSZ bilayer were fabricated by RF-sputtering. The single YSZ layer and YSZ/Ni-YSZ bilayer samples were annealed while the NiO-YSZ layer remained as-deposited. Cross-section transmission electron microscopy (TEM) samples of these thin-films were then prepared, which allowed detailed chemical and structural characterization of these thin-films on the nanometer-scale. Both YSZ and NiO-YSZ layers were fully dense and exhibiting equiaxed grain morphologies. Selected area electron diffraction (SAED) showed the YSZ crystal structure to be predominantly cubic in the annealed samples and amorphous in the as-deposited NiO-YSZ sample. It was found that YSZ film was 70 nm thick and dense, with equiaxed grains ranging from 12–20 nm. Surface roughness of the YSZ in the bilayer fell in the range of 5–20 nm. The Ni-YSZ film in the bilayer was 230 nm thick and porous, which consisted of columnar grains 13–75 nm in length and 9–22 nm in width. The bilayer sample showed no delamination or cracking along the YSZ/Ni-YSZ interface. It is believed that the nano-sized grains, minimal surface roughness and thin layers found in these films are desirable microstructural features for the anode and electrolyte in micro-solid oxide fuel cells (SOFCs). Correlation between microstructural features and electrochemical performance will be reported in a separate study.