The abilities to control the size, shape, composition, phase and surface properties of nanoscale catalysts are important for understanding the nanoscale properties of catalysts. Many existing methods in nanoscale catalyst preparation are however hampered by the lack of such abilities. This paper discusses the findings of an investigation of a molecularly-engineered preparation route based on synthesis, assembly and activation of supported monometallic, bimetallic and trimetallic nanoparticles. Such catalysts offer potential applications in fuel cells. Molecular engineering of the surface properties of the nanoparticles in terms of the particle-particle interactions and the particle-support interactions is a key element of our approach. Examples illustrating the role of this element in the wet chemical synthesis, molecularly-mediated assembly, and thermal activation processes of the supported metal and alloy nanoparticles will be discussed. The focus of these examples is the understanding of how size, shape, composition, phase, and surface properties of the nanoparticles evolve in each of the preparation stages, and how they are correlated with the activities and stabilities of the nanostructured catalysts.