The recent rapid advances in nanotechnology are due in large part to our newly acquired tools in measuring and manipulating nanostructures, even individual atoms or molecules. As a class of useful tools, scanning probe microscopy, especially scanning tunneling microscopy, provides us the special method to describe the locally physical and chemical properties of nanostructures, and even help us to manipulate nanostructures for constructing new nano-scale apparatus. Here we report our studies on fullerene molecules and quantum dots by using a ultra-high vacuum low-temperature scanning tunneling microscope with emphases on the following aspects: identifying orientational configurations of individual fullerene molecules on different material surface; novel topological order in 2-D C60 domains; single molecule manipulation and negative differential resistance molecular device involving two C60 molecules; size-dependent single electron tunneling effects in 2-D Au clusters; tunable single electron tunneling behavior of ligand-stablized 3-D gold particles; and electrochemical capacitance of a width-variable nano-junction.