A commercial femtosecond laser system operating at its fundamental wavelength (λ = 800 nm, near Infra-Red) was used to ablate both synthetic and natural quartz on polished and unpolished surfaces. Ablation rates and maximum depths were determined using two distinct optical setups: a 25 mm focal length Cassegrain reflecting objective, and a 50 mm focal length convergent coated lens. All samples were ablated with the same laser beam at E0 = 1 mJ, τ = 60 fs, f = 5 Hz and N = 10–8000 shots. The depth of ablation craters obtained with the lens shows a linear increase with shot number N up to N = 2000 shots. Then the depth increases much less with N and reaches a plateau above N = 3000 shots. Maximum depth was close to 1300 μm for N = 3000 shots. Using the reflecting objective, ablation rate starts from 0.42 μm/shot and decreases rapidly to 0.02 μm/shot at a maximum depth of 350 μm for N =1500 shots. Ablation thresholds (Fth) were calculated for 1 and 10 consecutive shots with energy increasing from E0 = 0.1–2 mJ/pulse. Threshold values varies from Fth=0.1 J.cm−2 (unpolished, 10 shots) to Fth = 2.9 J.cm−2 (polished, single shot). The energy penetration of IR-femtosecond laser pulses in quartz has been calculated at l = 271 nm. The low absorption of IR wavelengths in quartz affects the ablation efficiency in the first shots. The associated non-linear effects are visible on a crater FIB foil observed with TEM as progressive high-pressure photomechanical damage developing under the ablation pit. The present study emphasizes the potential of IR-femtosecond laser for ablation of highly transparent material, and provides reliable data for LA-ICP-MS applications in earth sciences.