Metal clusters arranged on nanostructured oxidized silicon wafers are presented as new model catalyst systems. A photoresist layer spun on top of a wafer was patterned by laser interference exposure. The grid obtained after removing the exposed parts of the resist is used as an etching mask. Hollows with diameters of 300 nm and depths between 50 and 60 nm were etched into the oxide layer using wet chemical methods. Two methods were applied to deposit metal clusters (Pd or Cu) in a defined way within the hollows. The particles ranged from 10 to 50 nm in height and from 80 to 200 nm in diameter. The model catalyst systems were characterized by atomic force microscopy and X-ray photoelectron spectroscopy. The method presented here allows us to produce 4 inch wafers that are covered completely by nanometer-sized structures in a reasonable period of time.