We demonstrate an elaborate method to controllably fabricate ultra-thin nanopores by layer-by-layer removal of insulating few-layer mica flakes with atomic force microscopy (AFM). The fabricated nanopores are geometrically asymmetric, like an inverted quadrangular frustum pyramid. The nanopore geometry can be engineered by finely tuning the mechanical load on the AFM tip and the scanning area. Particularly noteworthy is that the nanopores can also be fabricated in suspended few-layer mica membranes on a silicon window, and may find potential use as functional components in nanofluidic devices.