Sub-resolution assist features (SRAFs) damage-free cleaning by use of megasonic nozzle becomes main challenge in photomask industry. Using non-sulfate cleaning tool, the effect of key performance parameters of 1 MHz puddle megasonic nozzle such as megasonic power, and the gap between puddle nozzle and cleaned surface were investigated for opaque SRAFs sizes of 107 nm, 93 nm, 81nm, 71 nm, 63 nm, and 56 nm. Damage-free and high efficiency on particle removal cleaning for SRAFs size down to 71 nm for 38 nm technology node (MPU/ASIC ½ pitch, as outlined in ITRS 2010) has been demonstrated on advanced photomask with MoSi layer in this paper. Furthermore, conducting atomic force microscopy (CAFM) was employed to investigate the nanoscale surface electrical properties of chrome binary blanks cleaned by 1 MHz puddle megasonic nozzle. The results show that highly conducting regions on chromium oxide surfaces can be considered as "cavitation-rich and/or cavitation energy-strong" regions. And their sizes range from 15 to 100 nm, which are comparable to the sizes of SRAFs damage. Finally, in the future, CAFM may be a useful tool to inspect intrinsic defects on advanced photomasks at nanoscale, such as EUV blanks.