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Large three-dimensional (3D) mesocage structures that have multidirectional pore networks and uniform openings perpendicular to the longitudinal axis of NTs are of particular interest in terms of their potential. This paper reports on the feasibility of direct control of 3D mesopore cage structures throughout silica nanotubes (NTs) vertically aligned inside Anodic Alumina Membrane (AAM) nanochannels without the use of any organic stabilizing modifiers. This is the first reported study which uses direct synthesis of ordered cubic Im3m mesocage structures inside well-aligned silica-NTs that have open surfaces of top-bottom ends, and multidirectional (3D) mesopore connectivity. These 3D mesocage silica-NT arrays hybrid AAM channels function as nanofilters that can rapidly (in seconds) separate large quantities of proteins. In this nanofiltration assay, three proteins that differ in molecular weight and size such as …