Self-aligned silver nanocolumns embedded in amorphous Al2O3 matrix are produced by alternate pulsed laser deposition at room temperature in a single step process. The morphology and the spatial distribution have been investigated by standard, high resolution, and scanning transmission electron microscopy. Polycrystalline nanocolumns having diameters close to 3 nm and heights up to 7 nm are all oriented perpendicular to the substrate surface. The self-alignment of the nanocolumns is the consequence of the deposition of consecutive layers of Ag nanoparticles using the first layer as template for the ordered growth of the nanocolumns. Control over the density, diameter and height of the nanocolumns is achievable by tailoring the deposition sequence.