A study of morphological and composition changes of bimetallic (NiPd)/Si and 5x(Ni/Pd)/Si systems induced by laser pulses in picosecond time domain is presented. The effects of Nd:YAG laser, operating at 1064 nm wavelength with pulse duration of 150 ps, on a complex target were investigated. The laser- induced morphological and composition modifications have shown dependence on applied intensities and number of laser pulses. The results show an increase in surface roughness, formation of parallel periodic surface structures, appearance of hydrodynamic features and ablation of surface material. RBS analysis revealed that laser modification induced inter-mixing between the components of individual Ni and Pd layers, with indications of the formation NiPd intermetallic compounds. Interesting findings are the morphological changes include the formation of specific nanostructures in form of mosaic or parallel periodic structures.