A reversible concentration of nanoparticles in water solution is produced on a nanopore fabricated in situ by inverted-electron beam lithography (I-EBL) in a SiN membrane. The SiN membrane separated the water solution and a vacuum chamber of the EB system. The nanopore led to a small leakage of water that flowed to the vacuum chamber. This flow led to the collection of the nanoparticles within an area of less than 3 µm surrounding the nanopore. Then, the EB-induced Coulomb force rapidly released the nanoparticles from only the targeted nanopore. This electron beam direct manipulation of the nanoparticles can provide simple in situ microfluidics in analytical methods for biochemistry.