Embodiments of the invention relate to a method of functional materials deposition using a polymer template fabricated on a substrate. Such template forms an exposed and masked areas of the substrate material, and can be fabricated using polymer resists or Self-assembled monolayers. Deposition is performed using an applicator, which is fabricated in the shape of cylinder or cone made of soft elastomeric materials or laminated with soft elastomeric film. Functional materials, for example, metals, semiconductors, sol-gels, colloids of particles are deposited on the surface of applicator using liquid immersion, soaking, contact with wetted surfaces, vapor deposition or other techniques. Then wetted applicator is contacted the surface of the polymer template and rolled over it's surface. During this dynamic contact functional material is transferred selectively to the areas of the template. Patterning of functional material is achieved by lift-off of polymeric template after deposition. According to another embodiment, where self-assembled monolayers are used as template, selective deposition of functional materials is achieved either due to low surface energy of SAM or reactivity of terminal groups.