Not the author of this paper but am current PhD student focused on viroid discovery. There's no TEM but there are good methods such as RNAfold [0] for predicting their structures. In the case of rod-shaped RNAs, the prediction methods are quite good since it basically comes down to looking for substrings of reverse complement sequences within the circular RNA.
[0]: http://dx.doi.org/10.1186/1748-7188-6-26