Polymer Pen Lithography (PPL) is a low-cost, high-throughput direct patterning method to generate micro- and nanoarrays of chemicals on an underlying substrate. By simply changing contact pressure and the time of delivery, dots of various diameters can be produced. The unique AFM platform of Park Systems’ XE Technology with decoupled XY and Z scanners enable a very flat and linear XY scan over a large area, less than 2 nm out-of-plane motions over 100 µm x 100 µm and less than 10 nm out-of-plane motions over 400 µm x 400 µm. Therefore, precise control of a contact force and a contact time can be made with the flat and linear XY scan. With long range Z scan movement, it can also realize a wide dynamic range in pattern size from 50 nm to 25 µm.