Two-dimensional (2D) arrays of nanometre scale holes were opened in thin SiO2 layers on silicon by electron beam lithography and chemical etching. Oxidized silicon wafers with a 5 nm thick SiO2 layer on top were used in this respect. Pattern transfer involved either only removal of SiO2 or a two-step process of oxide removal and anisotropic silicon chemical etching to form nanometre scale silicon V-grooves. The size of the holes in the photoresist layer varied in the range 40–80 nm, depending on the exposure dose used. The smallest holes in the oxide were about 50 nm in diameter, while in V-grooves the smallest width was nm. 2D arrays of Ge dots or Ge/Si hetero-nanocrystals were selectively grown on these patterned silicon wafers. In small windows only one Ge island per hole was nucleated.