I admit that when I first saw this string of alternating consonants and vowels, I could make no etymological connections. What other words contain the root nid?
I couldn't think of any.
I wasn't even sure whether the last three letters marked it as a verb (like pontificate) or an adjective (like delicate).
The nid- in nidificate comes from the Latin word nidus "nest." Nidificate means "to build a nest," and the act of building a nest is nidification.
Certainly, there are enough birds around to keep us using nidificate in its literal sense, but I don't like to limit words that way. Expanding into the metaphorical, nidificate and nidification might well describe a child's burrowing into a pile of stuffed animals for the night, a cop settling in for a long stakeout, or a sniper arraying his perch to await the arrival of his victim.
A related word is nidiculous, which looks like a typo for ridiculous and means either "reared in a nest for some time" or "sharing the nest of another animal." Metaphorically, the word could be used, in the first sense, to describe one's offspring or, in the second sense, an adulterous spouse.