Vertical arrays of sealed nanofluidic channels, in which both cross-sectional dimensions are controllable down to 10 nm, were fabricated by selective side etching of a SiGe heterostructure comprised of layers of alternating Ge fractions. Capillary filling of these nanochannel arrays with fluorescent dye solutions was investigated using a confocal microscope. The feasibility of using nanochannels for size-based separation of biomolecules was demonstrated by imaging aggregates of tagged amyloid-beta peptide. The ability to integrate a large number of nanochannels shows promise for high throughput applications involving lab-on-a-chip systems.