Preparation and characterization of microscopic biochemically active regions are important for the development of miniaturized bioanalytical systems with proteins, such as miniaturized enzyme electrode arrays. Scanning electrochemical microscopy (SECM) has emerged as an ideal tool for prototyping such systems. The technique is based on electrochemical conversions of dissolved species at a micrometer-sized probe electrode. It offers several mechanisms for local surface modifications under conditions compatible with conservation of protein functionality of enzymes and antibodies. The subsequent imaging of the immobilized activity provides direct information about local immobilized enzyme activities. The working modes of the techniques are illustrated by recent studies from this laboratory for the design and characterization of patterned enzyme layers covalently linked to gold surfaces via thiol self-assembly chemistry.