Given that we break molecules down to atoms on a regular basis, the correct answer can only be along the lines of “Ya, sure, you-betcha.”
A molecule is a group of atoms held together by bonds. There is nothing physical to a bond, it is just a low-energy arrangement that makes it stable in its surroundings. All it takes to break a bond is energy. That energy can be supplied chemically, or by heat, light, sound…in short, any form of energy can break a bond so long as it is intense enough.
When a scientist wants to break a molecule down to its constituent atoms, heat is the most common approach. An intense flame or plasma at temperatures exceeding one thousand degrees does the trick quite nicely. In the lab, this is most often done when the scientist wants to see what metals are present. The heat serves first to break the molecule down to atoms. In techniques such as AES (atomic emission spectroscopy) and ICP (inductively coupled plasma), the heat can be further applied to identify some of the elements present. Every element has a unique spectrum of light that it emits when it is “excited”. (Think of it like a fingerprint for each element.) The same heat that breaks down the molecule also provides the energy to excite the atoms. From the light they give off, the scientist can tell which elements are present, and even in what amount.
Do recognize that during this whole process, the number of atoms never changes. If a molecule is made of 12 atoms (like isopropanol, which is made of 3 carbons, 8 hydrogens, and 1 oxygen), then it is broken down into those 12 atoms. The atoms do not change identity during the process, which is only a chemical reaction, not a nuclear reaction. The atoms may not stay solo for long. For many it is a higher energy arrangement, and so they will readily react with anything at hand that will produce a lower energy state. Namely, they make bonds and form molecules again. Not necessarily the same molecules though. In fact, it is most likely that small molecules would result. (From the isopropanol example, water, carbon monoxide, and carbon dioxide are likely candidates for the aftermath. The odds are strongly against isopropanol, a more complex molecule, reforming on its own.)
Many elements are naturally found as a part of molecules. Without the ability to break them apart, it would be difficult to obtain a number of the less common metals. Magnseium salts, for instance, are ionic compounds – molecules. To recover magnesium metal (a coherent collection of magnesium atoms), those salts which are dissolved in sea water (which breaks the ionic bond) and then the magnesium is reduced (electrical energy is used to give it back its missing electrons) to make the individual metal atoms. If there were no such mechanism, once an atom had been used once in a molecule, it would be forever unavailable for use again. All things considered, it’s a very good thing that atoms can be reclaimed from molecules.