Free-standing polymer (poly(methyl methacrylate) or cyclic olefin copolymer) nanopillar and nanotube ensembles with previously unreported, ultrahigh aspect ratios (300 to >1600) were fabricated via anodic aluminum oxide (AAO) template-based methods that utilize a dilute, aqueous H3PO4 template etchant followed by freeze drying removal of the aqueous medium. Good replication of the AAO template by either solutions of the polymeric materials or molten polymer was achieved by using ultrasonic degassing and vacuum conditions. Classical surface wetting and viscoelastic fluid rheology theories were applied to explain the formation of polymer nanopillars and nanotubes in the aluminum oxide templates. The utilization of dilute H3PO4 for etching the AAO template and freeze-drying removal of the environmental liquid allows for the preparation of free-standing, erect, and ordered polymeric nanopillars or nanotubes that show much promise for use in biological microelectromechanical systems that target biological analyses.