We demonstrate that nanocrystalline diamond films grown on highly doped silicon substrates can be patterned using a CO2 laser operating at a wavelength of 10.6 μm, where both low doped silicon and diamond exhibit negligible optical absorption. The patterning is initiated by free carrier absorption in the silicon substrate and further enhanced by the thermal runaway effect, which results in surface heating in the silicon substrate and subsequent thermal ablation of the diamond film in an oxygen rich atmosphere. Using this approach, micron-scale grating and dot patterns are patterned in thin film diamond. The localized heating is simulated and analyzed using concurrent optical and thermal finite element modelling. The laser patterning method described here offers a cost effective and rapid solution for micro-structuring diamond films.