In this paper we present studies on the optical transmittance of modified fused silica substrates subject to mask making dry etch and wet clean processes, mask handling, and photon chemical clean. Using a custom built nitrogen purged in-situ transmittance measurement system with a 172-nm Xe Excimer lamp photon chemical clean unit we have achieved measured transmittance up to 87% because of the removal of surface contamination. We concluded from the experiments that: (1) Transmittance of the as-shipped mask substrate is lower than that after the photon chemical clean, (2) Chromium dry etch not only caused a transmittance loss but also made the transmittance uniformity worse, (3) Acidic wet clean must be done after the Chromium etch to recover transmittance loss and uniformity problem due to contamination introduced in Chromium etch, (4) Long time storage (more than 30 days) and short term handling (a few minutes) in ambient condition both degrade transmittance. We found that in-situ transmittance measurement after the photon chemical clean is needed in order to eliminate the transmittance measurement uncertainty due to surface contamination
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