A versatile method for parallel nanoscale structures fabrication and patterning, using a combination of stencil-mask and pulsed-laser deposition (PLD) techniques is presented. A miniature shadow-mask with nano-apertures in a very thin microfabricated membrane (nanostencil) was separately manufactured and then, mechanically attached to the substrate of choice. In this way, complex oxides such as BaTiO3, BiFeO3 and PZT were deposited directly through the stencil’s holes onto various substrates (Si, Pt coated Si, SrTiO3). Controlled arrays of nanostructured complex oxides were obtained as copies of the aperture patterns in the stencil membrane in a single deposition step. The morphology and composition of these nanostructures were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM) and X-ray diffraction (XRD). Analyses reveal periodic, wholly separated and well-defined structures over large areas corresponding to the entire openings in the nanosieves (1mm length x 100 um width). This approach offers a reliable, parallel method for growing, patterning and positioning ferroelectric functional nanostructures on various substrates, an issue of wide interest for applications in microelectronics, especially in Ferroelectric Random Access Memories (FeRAM). It also represents a promising “tool” for local deposition of multiple geometries and high-purity nanostructures under high-vacuum or ultra-high vacuum conditions, in laboratories without expensive lithography equipment.