A thiophene-terminated alkanethiolate self-assembled monolayer was studied by metastable atom electron spectroscopy (MAES)and infrared reflection absorption spectroscopy (IR-RAS). Since MAES is an extremely surface selective method, it allowed us to determine which part of the molecule is exposed to the outside of the surface in a monolayer. Theoretical simulation with partial exterior electron density suggested that not only the thiophene group but also a part of the main chain are exposed to the outside, indicating the bonding to the substrate with thiolate formation. The selection rules of IR-RAS demonstrate that the plane of the thiophene ring is almost lying parallel to the surface and that the alkyl chain aligns nearly along the surface normal. These results are consistent with the findings in our previous X-ray photoelectron spectroscopy study that the molecule is adsorbed with forming thiolate in a densely packed manner.