AbstractChemically patterned surfaces for biotechnology applications often require sub‐micron patterns to match specific sub‐cellular structures and control the presentation of proteins to single cell arrays. Plasma polymer coatings are used extensively in the biotechnology sector for biomaterials, cell culture and tissue engineering, but their patterning has not been investigated at the sub‐micron level. The resolution limit of plasma polymerized patterns with designed line widths of 900 to 20 nm is investigated via dual chemistry patterns of plasma polymerized acrylic acid and allylamine created with poly (methyl methacrylate) resist and electron beam lithography (EBL). Line widths are characterized via scanning electron microscopy and atomic force microscopy with surface chemistry analysis via time‐of‐flight secondary‐ion mass spectrometry (ToF‐SIMS). The smallest line width measured is 29 nm for a designed line width of 20 nm. High‐resolution nanoscale imaging is achieved using ToF‐SIMS, with lines down to ≈60 nm in width visible. This work demonstrates the successful fabrication and characterization of sub 100 nm dual plasma polymer patterns using EBL, establishing a clear route for large scale production of plasma polymerized nanopatterning.