Synchrotron-based X-ray photoemission electron microscopy (X-PEEM), atomic force microscopy (AFM), time of flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS) have been used to visualize and characterize plasma polymerized acrylic acid (ppAA) and poly ethylene oxide (PEO)-like microstructures. Micropatterned microstructures have been fabricated with electron-beam lithography to obtain contrasted ppAA/PEO-like structures. A surface area of 500 µm × 500 µm was patterned with arrays of 5 µm diameter circles and 500 µm × 5 µm lines. Samples have been analyzed before and after immersion of ubiquitin protein solutions. AFM and X-PEEM results indicated that the protein adsorbed preferentially on the ppAA regions for both circular and line patterns. For both circular and line patterns, the protein preferentially adsorbed to the ppAA regions. Copyright © 2010 John Wiley & Sons, Ltd.