By means of high-resolution transmission electron microscopy (HR-TEM) observations, and energy dispersive X-ray analyses performed with a scanning TEM (STEM-EDX), we evaluated the residual Na contents and the induced crystal strains in type-II Si clathrate films grown on a Si substrate and treated with iodine for Na elimination. Cross-sectional, TEM and STEM-EDX observations verified the formation of the type-II Si clathrate thin film on the Si substrate. The guest-free (without any Na inclusion) clathrate crystal was obtained by iodine (I-2) treatment for more than 3 cycles. The resulting films were polycrystalline. No buffer layer was observed at the boundary of the Si clathrate crystal film and the substrate, suggesting a chemical bonding between them. The crystalline strains defined here by the deviation of the d value were within 3.5%. These findings might allow us to fabricate epitaxial Si clathrate films on Si substrates. (C) 2016 Elsevier B.V. All rights reserved.