Why not to try using size-exclusion chromatography?

Good idea

but i need to handle several samples simultaneously. I think ultrafilteration is more convenient.

The molecular weight of a 100 nt RNA is over 30 kDa and is most likely extended in shape. If you want to use ultrafiltration to get rid of it, you will have to use a high molecular weight cutoff, at least 100 kDa, preferably higher. If your RNPs are large enough that they won't go through the filter, then it may work.