There are about 103 basic elements, or kinds of atoms. When a few atoms are combined they form molecules. Water is not one of the 103 basic elements or kinds of atoms, it's something new, more complicated, that is made by combining atoms. This three-atom molecule of water is so small that it would take a special microscope to see it. Nanotechnology is the theoretical side of atomic manufacturing, and molecular manufacturing.
Molecular manufacturing is the ability to make or build things with molecules.
You can also take things apart down to their simplest molecules. Water in one bin, flour in another bin, sugar in another and so on. This is really great for recycling, even very bad chemicals, can be broken down into several bins of harmless molecules. You could also build the cake by putting the molecules together. It's called making a cake.