This work presents arrays of heterogeneous nanopillars stacked with Si bodies and SiO2 heads for biomedical applications. Novel crossed and overlapped spacer techniques are proposed to fabricate the nanopillar arrays in controllable dimensions. For the nanopillars in the arrays, the minimum spacing, body diameter and head tip-radius reach 100 nm, 23 nm and 11 nm, respectively. The maximum height is 1.2 μm. In addition, because of hydrophilic/hydrophobic selectivity between the SiO2 heads and Si bodies, localized nanoliter water-droplet condensing, fluorescein solution extraction and protein capturing are observed on the SiO2 pillar heads. These experiments demonstrate the great potential of heterogeneous nanopillars in biomedical applications.