Handling of picoliter-to-nanoliter-scale volumes and objects has increasing importance in life sciences. This is the volume scale of cell extractions and individual living cells. Here, we introduce a method of generating a picoliter-scale device by direct writing of picowell arrays on a ZEONOR™ copolymer surface with high-energy medium-mass ion microbeam. Arrays of various microstructures were written in the sample using a microbeam of 10.5 MeV N4+ ions at various implanted ion fluences. The best array was obtained by implantation of annuli of 10 and 11 μm of inner and outer diameters with a fluence of 7.8 × 1012 ions/cm2.