Types of fusion
Things we would desire for fusion energy productiona re among others:
- envirounmental friendliness
- low cost
- relatively small size and low weight
In how far may atomically precise technology be able to help in these regards?
For a basic introduction please consult the Wikipedia article about "magnetic confinement fusion" 
Field strength and plant size
The limit in achievable magnetic field strength has led to the construction giant prototype plants (see ITER). But tokamak devices can be scaled down greatly by raising the magnetic field that confines the plasma. Newer magnet technology (high temperature super conductors HTSLs) is promising some degree of notable size reduction (see company "Tokamak Energy").
It is yet unknown what kind of fields will be achievable once advanced APM gives us much more control over matter and lets us mechanosynthesize super-exotic thermodynamically metastable superconductor compounds.
It may not be unreasonable to assume that large margins for improvements are still possible but at this point this is highly speculative since it still critically depends on fundamentally unpredictable discoveries in science. It's hard to project how the performance of superconductors will further increase. This limits the range of possible serious predictions severely. (See: non mechanical technology path).
The penetrative power of some kinds of radiation may pose limits on attempts to scale down magnetic confinement fusion devices. See section "radiation damage" for more details.
- APT is great at dealing with very high levels of power density (see: Thermal energy transport).
High thermal power densities require refractory materials.
With high magnetic fields and high plasma densities power fluxes become very high. (Potentially higher than atmospheric reentry of a space-shuttle) On the other hand smaller devices feature much more wall surface area per enclosed volume.
Note that a significant amount of energy does not get deposited directly onto the chamber walls but into the volume behind mainly due to neutron radiation.
Extremely high magnetic fields cause extremely high mechanical forces. Both structural frame parts and structural superconductor carrier strips need to be very sturdy. (Structural superconductor carrier strips: Note that most of the cables do not carry the current but provide the necessary mechanical strength)
Wile even with the next generation of HTSL high field tokamaks steel can provide sufficient strength with even higher fields this might not be the case anymore.
Abundant elemental metals on the other hand are by far not strong enough. There are exotic metal alloys that are a quite a bit stronger than what is used now but they contain elements that are rather rare and thus way too expensive to use in excessive quantities.
Thus one will want to go to cheap metamaterials that are based on strong gemstones like
e.g. diamond (C), moissanite (SiC), colorless sapphire (Al2O2), ...
Those are hopefully strong enough. For all we know at the moment there cannot be anything much stronger than those.
By switching we incur a pretty severe problem though. Gemstones are much more susceptible to ionizing radiation than metals. Broken covalent bonds in gemstones are not always self healing like the electron-gas of metals can be.
There may be a workaround. See section "radiation damage" for more details.
One can speculate whether or not one could reduce the overall weight of a reactor far enough to make it suitable for application in spaceships. (investigation needed) Currently (2016...2018) it still pretty impossible to reach anything near light enough.
APT is bad at dealing with radiation. (See: radiation damage) And some parts of the radiation (especially neutron radiation) are very hard to shield.
Radiation threatens the structural integrity of the frame and perhaps more critically it could lead to a breakdown of super-conduction (quenching) due to an accumulation of faults in the superconductor material.
One could try to treat the cause or the symptoms.
Treating the cause:
One could try to target fusion reactions that do produce almost no neutrons (are mostly aneutronic). But it probably will be really desirable to archive the capability to run solely on the most abundant hydrogen isotope (protium 1H) (and other exotic fuel combinations).
Shielding is only possible in a limited sense. It cannot be influenced too much by the choice of materials.
Treating the symptoms
A solution to the rapid material degradation problem may be continuous active repair. A system that is continuously exchanging degraded structural microcomponents with new ones. Very unlike the normal use case where you want to avoid putting things together atom by atom every time anew and do microcomponent recycling instead. Here the massive inefficiency really is necessary and overcompensated by the reactors energy output anyway.
Designing such a pretty complex self repairing system would pose massive design effort. It should not be expected as one of the first products producable by advanced APM.
Without applying at least one of the two approaches the inherent penetrative strength of neutron radiation may pose a fundamental hindrance for scale-down. The requirement to absorb most of the neutron radiation before it reaches coils and cryo-system then creates a natural lower end size limit for magnetic enclosure fusion. But in many cases this might be ok for non mobile power plants, where ease of long term operation is of more importance than size and mass.
Albeit non atomically precise in nature molten salt blankets are probably a pretty good idea since the crystal structures of liquids do not incur any radiation damage since they have none. For the the vessels they are confined in its probably desirable to use gemstone based metamaterials. They may not carry high mechanical loads but unlike metals they do not corrode.
(wiki-TODO: treat the following topics in more detail)
- macroscopic vibration damping
- neutral particle carriage acceleration
- highly symmetric enclosement (thermal and quantum mechanical uncertainty)
- low reflectivity of hydrogen - minimal isolating plasma shell thickness (severe!)
- fast cavity cleanout
- fast radiation seals
- carriage particle accelerators
- small scale Laser particle accelerators
Sadly this does not work. Assuming a naive press-together-approach here. When pressing together two atoms with large mechanical force (possible with advanced mechanisms for mechanosynthesis) long before the nuclei get anywhere near** each other one of the strong covalent bonds breaks. One of the chemical bonds that holds in place the atoms with the to-fuse-nuclei within. => Fail. (**"near" in a relative sense -- nucleus-size to nucleus-to-nucleus-distance)
Not to mention that the due to the spacial confinement to the tip atom the zero-point-energy of the nucleus is so big that even near absolute zero of temperature its quantum delocalization is much bigger than its own size. So even if you could overcome the electrostatic repulsion with a pick and place approach (which is impossible as explained above) you would not get the nuclei to contact directly but only have a low density probability cloud overlap.
Highly speculative one try one hit fusion
Warning! you are moving into more speculative areas.
- Thermal throughput bottleneck thermal energy transmission
- self repair of thermal and radiation damage
- isotope sorting (e.g. tuning fork method) & closed loop nuclear waste recycling
- usage for spacecraft propulsion possible? - earth or space only?
- Implications of Liouville's theorem or "why nuclear mechanosynthesis don't work" - detour over thermal step unavoidable
- surface power/(heat flor) density limit - capsule based thermal energy transport (asymmetric figure eight loop in tokamaks?) may move it further down to more tacklable values.
- consistent high temperature stable designs SiC (H-passivation?)