We report on the characterization of modifications in fused silica after exposure to low fluence (2 J/cm2) 355 nm laser at repetition frequencies of 1 Hz, 5 Hz and 10 Hz. Synchrotron based XRF spectroscopy is employed to study concentration variation of metal inclusions in the surface layer. Positron annihilation lifetime spectroscopy is used to probe atomic size defects variation in bulk silica. FT-IR is used to characterize changes of bond length and angle of Si-O-Si covalent bond of irradiated silica. Compared to the basic frequency, the big loss of cerium and iron concentration, the size enlargement of vacancy cluster and the decrease of Si-O-Si covalent bond length after 10 Hz laser irradiation are illustrated by our data. These tiny modifications provide important data to investigate laser damage mechanism.