A reproducible wafer-scale method to obtain 3D nanostructures is investigated. This method, called corner lithography, explores the conformal deposition and the subsequent timed isotropic etching of a thin film in a 3D shaped silicon template. The technique leaves a residue of the thin film in sharp concave corners which can be used as structural material or as an inversion mask in subsequent steps. The potential of corner lithography is studied by fabrication of functional 3D microfluidic components, in particular i) novel tips containing nano-apertures at or near the apex for AFM-based liquid deposition devices, and ii) a novel particle or cell trapping device using an array of nanowire frames. The use of these arrays of nanowire cages for capturing single primary bovine chondrocytes by a droplet seeding method is successfully demonstrated, and changes in phenotype are observed over time, while retaining them in a well-defined pattern and 3D microenvironment in a flat array.