We fabricated a large number of microscale via-hole structure molecular devices (2240 devices) using octane-Se [CH3(CH2)7Se] self assembled monolayers (SAMs) and compared their charge transport properties with those of octane-S [CH3(CH2)7S] SAMs molecular devices in terms of current density, resistance, and tunneling decay coefficient. The device yield of the "working" octane-Se molecular devices was found to be approximately 1.7% (38/2240), which was similar to the yield of approximately 1.1% (50/4480) for octane-S devices. Our statistical analysis revealed that for octane-Se devices the tunneling current was slightly smaller and the low-bias resistance and decay coefficient were slightly larger than those for octane-S devices. The standard deviations of these transport parameters of octane-Se devices were found to be broader than those for octane-S devices due to irregularity of the binding sites of octane-Se on Au electrode surface.