A femtosecond pulsed Nd:YAG laser was used to micromachine polycrystalline diamonds (PCD) and study the ablated microstructure characteristics under different irradiation parameters. With high laser intensity and low traverse speed, a micro cone with very smooth surface and clear edge can be obtained. There was almost no recast layer around the cone and no phase transition on the ablated surfaces was found. By contrast, the use of low laser intensity and high traverse speed could ablate only the grain boundaries without any damage to the diamond grits. These results suggest a need for further research in femtosecond laser micromachining of PCD for potential applications in fabricating new types of micro grinding wheels or diamond pencils.