Nanopores embedded in a thin membrane with diameter below 10 nm are suitable for the biomacromolecule detection. For such purpose, in this study, we developed a technique of how to obtain small nanopores in silicon nitride films using a focused-ion-beam (FIB) system. By changing the process parameters, such as the beam current, the film thickness of the membrane and the ion beam exposure time, the diameter of the nanopore can be tuned. Under an optimized condition, high quality nanopores with diameter as low as 6 nm was fabricated on a 7 nm thick membrane. Our result suggests that FIB direct writing technique might be a suitable approach for biomacromolecule detector fabrication.