The present invention relates to a process for producing a 3-dimensional structure assembled from nanoparticles by using a mask having a pattern of perforations, which comprises the steps of: in a grounded reactor, placing a mask having a pattern of perforations corresponding to a determined pattern at a certain distance above a substrate to be patterned, and then applying voltage to the substrate to form an electrodynamic focusing lens; and introducing charged nanoparticles into the reactor, the charged particles being guided to the substrate through the pattern of perforations so as to be selectively attached to the substrate with 3-dimensional shape. According to the process of the present invention, a 3-dimensional structure of various shapes can be produced without producing noise pattern, with high accuracy and high efficiency.