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A flexible method for simultaneous nanoscale structures fabrication and patterning is described, using a combination of stencil mask and pulsed-laser deposition (PLD) techniques. A miniature shadow-mask with nano-apertures in a very thin microfabricated membrane (nanostencil) was first manufactured and then, mechanically attached to the substrate of choice. To create free-standing membranes with arrays of apertures of different shapes and dimensions below 500 nm, a combination of advanced lithography or high-precision ion milling by focused-ion-beam (FIB) and silicon micromachining techniques was used. Using PLD, complex oxides such as BaTiO3 and BiFeO3 were deposited directly through the stencil’s holes onto various substrates (Si, Pt, SrTiO3 and SrRuO3). Ordered arrays of nanostructured complex oxides were obtained in a single deposition step, which replicate the aperture patterns in the stencil membrane. 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, entirely separated and well-defined structures over large areas corresponding to openings in the sieves (1mm length x 100 um width). Ferroelectric properties of the patterned structures of different sizes were investigated by AFM piezoresponse method in order to study size effects in ferroelectrics. Pulsed laser deposition parameters as well as the geometrical attachment of the stencil onto the substrate are important factors that must be tuned during the process in order to increase the steepness of the structures. Several other issues related with the deposition process such as large scale uniformity and periodicity of deposited nanostructures across the substrate and the stencil’s life time were also investigated and will be presented and discussed. This approach offers a simple, reliable, parallel method for growing, patterning and positioning ferroelectric functional nanostructures on various substrates, which is of wide interest for applications in microelectronics, for instance for 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.