Nanometer scale pits have been fabricated in a crystalline fatty acid monolayer by applying weak repulsive force exerted from the cantilever tip of an atomic force microscope. In this method, the shape of fabricated pits was controlled to be circular or rectangular. The minimum diameter of the pit was similar to 20 nm. It was demonstrated that the pits could be artificially distributed with different size and surface area density in the organic monolayer.