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Highly stable nanopores with precise size and film thickness are essential for ultrasensitive molecular biosensors and efficient ion filters. However, the stability of both solid-state nanopores and biological nanopores is of a few hours. Even for two-dimensional (2D) materials with excellent properties, it is very difficult to prepare nanopores with stability for more than 1 day. Here, in mechanically exfoliated 2D materials with excellent quality, highly stable nanopores have been fabricated. Through the manual control of defect density and laser spot irradiation, the breakdown process is more controllable. The nanopore diameter can be precisely adjusted from 1 to 10 nm. The 2 nm thick graphene nanopore (with a diameter of 2 nm) maintains good consistency in conductivity during the 1-month immersion in KCl (1 M) solution. The pore size changes less than 0.7% per day. We found that 2D material nanopores can produce a strong rectification ratio (~50) due to the morphology undulation. In addition, our devices can recognize modified 5 nm Au nanoparticles, showing great potential for single-molecule detection. This work can guide the development of high-quality ion rectifier devices and biosensors based on 2D material nanopores. [ABSTRACT FROM AUTHOR]