A key question for any new technique is defect levels. With self-assembled methods, there is a reduction in free energy gained by the organizing of the molecules; but, after initial application of the material, the molecules are usually not in the minimum energy arrangement. Some sort of annealing step is needed to enable the molecules to arrange themselves in a way that minimizes free energy. If the free energy reduction by reaching the optimum arrangement is small, then thermal energy from the environment, as measured by kT, can cause random rearrangements away from the desired configuration. In this case, defects can spontaneously form or cannot be annealed out because further annealing starts creating new defects at the same time as other defects anneal away. For DSA, it has been shown that the free energy penalty of creating a defect is large enough that annealing can produce defect free structures 
. However, for DNA origami, this is reported not to be the case 
. For the bottle brush polymers, no such data is available.
The self-organizing systems described above are of different types. The bottle brush polymers basically provide imaging pixels. In the described work, the individual pixels aren’t aligned to any guide structures. The pixels are circular rather than square or some other shape, and the resolution is not as small as the pixels because cross linking of the cylinders is used to create the pattern after development. In theory, the cylinders could be aligned to guide structures and the pixels could have a different shapy using some clever (but as yet unknown) chemistry. Assuming this could be done, there would still be some limitations. Printed CDs would have to be an integer fraction of the feature size, and there would be a tradeoff of pixel size and feature size. Large pixels would give less roughness, but constrain the dimensions you can print. Small pixels would enable a wider range of dimensions but provide more random feature edges. What is more, the mechanism doesn’t enable smaller features than the aerial image provides. You may get cleaner patterns than with ordinary photoresist, but it this may not be valuable enough to make this effort worthwhile.
In DSA there also defined domains, and in some cases, such as vertical domains that are cylindrical, they can be thought of as pixels. In other cases, such as with lamellae or with horizontal cylinders, the domains are close to infinite in length and are not typical pixels at all. But a printed pattern is one domain wide, so the edge of the pattern is determined by molecular effects at the edges of domains, and the edge roughness is not directly related to the domain size. In DNA origami, the patterns have boundaries that are related to the DNA molecular structure and should not suffer from patterning noise. However, there may be some pattern transfer noise. In the cited example, even though the opening in the DNA were square the transferred patterns were more circular.
In all of these examples, the position of the final pattern is a challenge. The bottle brush polymers do not line up on a preferred grid and this adds variation in the positions of the edges of a printed pattern. The other two methods use a guide pattern to control placement, but there is noise in the alignment of the organized molecules to the guide pattern which adds to the alignment error already present due to the overlay variation in the printing process. Overlay is already a key challenge in moving to smaller critical dimensions. Future nodes have projected overlay requirements for three sigma overlay of less than 2nm. Meeting this target is a challenge for all organized molecule methods. It’s not enough that molecules self-organize into useful patterns. They have to self-organize in the right places.