A set of recommendations to maintain high activity of immobilized enzymes is developed based on direct observation via AFM. This helps to close knowledge gaps that often lead to poor performance of nanobiocatalysts for chemical synthesis. Molecule-level height and volume distribution analyses from high-resolution AFM images were applied to Candida antarctica Lipase B (CALB), subtilisin Carlsberg, and the Lipase from Thermomyces lanuginosus (TLL) deposited on model silica surfaces. Ensembles of flexible or "soft" enzymes appear separated when interactions with the surface are considerable at low surface coverage but form highly entangled structures of increased conformational stability at high surface coverage. By contrast, ensembles of rigid or "hard" enzymes appear to maintain stable aggregates even under strong interaction with the surface. The more rigid the enzyme the higher its tendency to remain in a densely packed state that is able to withstand surface-induced conformational transitions detrimental to catalysis. Weakening of surface-protein interactions for "soft" enzymes will prevent single-molecule immobilization, which reduces catalytic competency through structural changes. Multi-layer coverage in enzyme immobilization should generally be avoided due to mass transfer limitations. (C) 2014 Elsevier Ltd. All rights reserved.