Despite significant improvement in separation efficiency using nanostructure-based platforms, the mechanism underlying the high efficiency of rare cell capture remains elusive. Here we report on the first mechanistic study by developing highly controlled nanostructures to investigate cell surface nanomorphology to better understand the cellular response of CD4(+) T-lymphocytes in contact with nanostructured surfaces and to elucidate key mechanisms for enhancing separation efficiency. Our results showed that actin-rich filopodia protruded from T-cells in the early stage of cell capture (<20 min), demonstrate the different morphologies in response to various quartz nanopillar (QNP) arrays functionalized with streptavidin and the generation of sufficient adhesion sites for rendering more stable binding through three-dimensional local nanotopographic interactions between filopodia-QNPs and cell-substrate, leading to synergistic effects for enhancing cell-capture efficiency. This responsive mechanism of T-cells on nanotopographic templates provides new insights to understand the enhanced cell-capture efficiency and specificity from the primary cell suspension on nanostructured substrates.