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We constructed an effective vibration isolation system that employed an active vibration isolation system on top of a thick base-slab foundation and evaluated the performance by comparing the resultant vibration levels with the most stringent criterion of architectural standards (VC-E). The effect of the thick base slab on reducing vibrations was systematically investigated by comparing vibration levels at the bedrock with those at the base slab. The vibration spectra measured on the active vibration isolation table achieved an overall 1/100–1/200 of the VC-E in the range of 1–100 Hz, except at 5–25 Hz in the vertical direction. In addition, these vibration spectra were compared with those from another vibration isolation system based on a separate foundation. These comparative studies of vibration isolation, including details of the entire systems, can provide useful information for designing an effective vibration isolation system for various experiments that are highly sensitive to low-frequency vibration noise, such as scanning probe microscopy, electron microscopy, and ultrafine patterning.