This study presents a comparison of two types of bifunctional structured surface that were made from the same polymer –– an antimicrobial polycation (a synthetic mimic of an antimicrobial peptide, SMAMP) and a protein-repellent polyzwitterion (poly(sulfobetaines), PSB). The first type of bifunctional surface was fabricated by a colloidal lithography (CL) based process where the two polymers were immobilized sequentially onto pre-structured surfaces with a chemical contrast (gold on silicon). This enabled site-selective covalent attachment. The CL materials had a spacing ranging from 200 nm to 2 µm. The second type of structured surface (spacing: 1 – 8.5 µm) was fabricated using a microcontact printing (µCP) process where SMAMP patches were printed onto a PSB network, so that 3D surface features were obtained. The thus obtained materials were studied by quantitative nanomechanical measurements using atomic force microscopy (QNM-AFM). The different architectures led to different local elastic moduli at the polymer-air interface, where the CL surfaces were much stiffer (Derjaguin-Muller-Toporov (DMT) modulus = 20 ± 0.8 GPa) compared to the structured 3D networks obtained by µCP (DMT modulus = 42 ± 1.1 MPa). The effects of the surface topology and stiffness on the antimicrobial activity against Escherichia coli, the protein repellency (using fibrinogen), and the compatibility with human gingival mucosal keratinocytes were investigated. The softer 3D µCP surfaces had simultaneous antimicrobial activity, protein repellency, and cell compatibility at all spacings. For the stiffer CL surfaces, quantitative simultaneous antimicrobial activity and protein repellency was not obtained. However, the cell compatibility could be maintained at all spacings. The optimum spacing for the CL materials was in the range of 500 nm–1 µm, with significantly reduced antimicrobial activity at 2 µm spacing. Thus, the soft polymer network obtained by µCP could be more easily optimized than the stiff CL surface, and had a broader topology range of optimal or near-optimal bioactivity.