The use of catalytically active nanoclusters as a novel material for atomic force microscope (AFM) nanolithography is demonstrated. Films were prepared from colloidal Au nanoparticles and giant Pd clusters. Lithographic patterns were generated using the contact area of the AFM tip to physically displace nanoclusters, forming two-dimensional patterns on silicon oxide and functionalized silicon surfaces. Linewidth was found to depend on the force applied to the nanoparticles and the number of tip passes used to generate the pattern. Conditions were optimized to clear scanned areas using minimum applied force. Patterned films were used as templates for the selective deposition of electroless metal, which served as a robust plasma etch mask for pattern transfer into the underlying substrate to a depth of 200 nm. Minimum linewidths of approximately 35 nm were achieved in etched samples.