If they are Boston ferns or their kin, there is no harm in removing the thin rhizomes. If it is a rabbit's foot fern or a macho fern, or another one with thick rhizomes with fronds like them, removing the rhizomes may weaken the plant. Therefore, if you need to remove some, don't take more than 1/4 of the longest ones every 6 months.

Thank you Tugbrethil, I didn't think about removing them! Now I can re-pot them confidently.

Lawsy! I have to stop going online while I am asleep! If it's the slim rhizomes, you can keep them in, or let them hang out, or cut them off as you please. The thick rhizomes should be laid on the new soil surface, and over the edge of the new pot. Should be pretty easy--knowing how should sometimes goes! :)