In this paper, we present the observation results of the surface potential of micropatterned thick (> 1 μm) self-assembled electrets (SAEs) for MEMS vibrational energy harvesters (VEHs). To evaluate the surface potential of micropatterned SAEs, we propose and develop test devices with removable through-hole substrates corresponding to the moving electrodes of SAE-MEMS VEHs. In this study, SAEs are deposited simultaneously on two test devices with different through-hole spacings and on a reference flat substrate using the same vacuum evaporation process. The surface potential of SAEs is proportional to the film thickness, and when the film thickness of the SAE deposited on the flat substrate is 4.48 μm, the surface potential exceeds 200 V. At this time, in a test device where the average thickness of micropatterned SAEs is 3.08 μm, the measured surface potential is 68 V. In addition, it is experimentally observed that when micropatterned SAEs are formed using the through-hole structures, the microfabrication process causes the SAE pattern to spread wider than the through-hole dimensions, and the surface profiles are not flat. These findings provide useful insights for the design of SAE-MEMS VEHs using micropatterned SAEs with through-hole structures.