Abstract Structures of silica particles on a titania surface and titania particles on a silica surface were formed by deposition of SiO2 or TiO2 nanoparticles on pre-patterned substrates. Photolithography was used to create a matrix for the selective deposition of nanoparticles by immersion in a colloidal suspension. Atomic force microscopy was used to investigate the topography of these inorganic assemblies. Whereas two-dimensional colloidal patches of TiO2 nanoparticles are obtained on silica surfaces, SiO2 nanoparticles form three-dimensional, U-shaped channels on titania surfaces. The influence of electrostatic forces on assembly structure is vital. The isoelectric points of the particles, the pre-patterned matrix and the photo-resist are key parameters and may be manipulated to achieve various microstructures. The 2D nanoparticle arrays of titania on silica and 3D channels (built of silica nanoparticles) on flat titania surfaces are of potential interest in lab-on-a-chip applications.