This paper demonstrates the fabrication of a membrane permeated by a silicon dioxide nanocapillary array for manipulating highly charged ions at the nanoscale. The fabrication method involves (i) the formation of pores at the nanoscale on lithographically patterned, n-type silicon using photo-assisted electrochemical etching, followed by (ii) thermal oxidation, (iii) bulk silicon back etching and (iv) oxide etching using silicon micromachining technology. The electrochemical etching parameters were chosen to form arrays of straight pores with a diameter of about 250 nm, a length of 30 µm and interpore distances of 1 and 1.4 µm. The back side of the pore arrays was etched in potassium hydroxide and tetramethyl ammonium hydroxide. Finally, the inside of the pores was thermally oxidized to yield SiO2 capillary arrays. The present method could allow the fabrication of capillaries with further smaller dimensions by increasing the thermally grown oxide thickness.