The present invention relates to a continuous process and a system for macromolecular assembly and capture (refolding or proteins (e.g. refolding of HAT human .beta.2-microglobulin), hybridization of nucleic acid, nucleic acid analogues, and protein-nucleic acid chimera, aggregation of carbohydrates, and assembly of nanostructures/nanomaterials. The process may comprise the steps of providing fluid compositions comprising at least one of said macromolecular substances in a predominantly unassembled form, providing a dispersion comprising coated, essentially non-porous magnetic particles, combining said fluid compositions and the dispersion of magnetic particles thereby providing a continuous stream, passing said continuous stream through a first mixing device thereby forming magnetic complexes each comprising a magnetic particle and a plurality of macromolecular assembly species; passing the continuous stream through a first capture compartment of a magnetic separator thereby capturing said magnetic complexes; and separating said magnetic complexes from said continuous stream, and isolating said macromolecular assembly species.