Atomically precise disassembly
In advanced atomically precise manufacturing systems the capability of general atomically precise disassembly is not a necessity. In contrast to mechanosynthesis atom by atom disassembly can be a much harder problem.
(TODO: Mechanosynthesis can be made to be highly energetically reversible (efficient). How does this relate to reversing the reaction?)
Disassembly of diamondoid products
When atoms are placed into e.g. a stable diamondoid crystal lattice they form multiple bonds. To get them out again one would need to bind them even stronger to the tooltip. But thats (seems) not possible anymore since there are no single bonds that bind stronger than three carbon-carbon bonds (maybe a counterexample with silicon ). So once placed in most cases the atom stays stuck until the whole part in which it resides in gets burnt. (See: Diamondoid waste incineration) With materials that have weaker bonds and or are more loosely meshed one might have more luck disassembling but there are other problems.
Note: Experimental results may suggest otherwise. (wiki-TODO: ref Si Sn exchange paper)
Disassembly of natural products
For materials which do not have diamondoid character (e.g. chain polymers, metals alloys) cryogenic temperatures are needed so that everything stays put. Many natural materials are very unordered, have some of their atoms diffusing around and they also have crystal defects making it necessary to scan the surface and have a plan for every possible situation which might occur. A very difficult problem way beyond the scope of in relation simple APM attainment projects.
To simplify matters preceding conventional thermal processing methods may help a lot. Usually the goal is to get only a view types of rather small molecules. (See: Unknown matter claimer and Diamondoid waste incineration) Preprocessing devices may also be subject to improvement and miniaturization from the megascale to the meter scale. (Better thermal isolation, higher pressure capacity, ...) But no further miniaturization down to micro and nanoscale due to inherent complexity.
- APM aided oil refinement: refining crude oil on a much smaller (but not nano) scale
- waste water treatment - a device locally in your own basement - also not partly not operating way above nanoscale.
- handling of crude substances in general - mining - old aluminum - ...