When we denude something we strip it, like the branches of a tree. That seems a bit inverted to me, shouldn't it be to nude-something?
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Prefixes can have multiple uses. In the case of denude:
Because sometimes Latin’s de- prefix meant something else than to strip something away or to undo or reverse the action of a verb. And so it also has come down to us as something else in English.
You were thinking of OED sense 6, so here are the OED’s senses 3–5 for de- to illustrate just a few of the other possibilities for that prefix:
There actually is a word that is constructed and means what you seem to be expecting of denude, and that is debare. Again per the OED:
As you see, it hasn’t been used much for quite some time. The OED labels it obsolete. Best stick with denude.
Though tchrist's answer is clearly correct, and the OED's sense 3 of de- governs the word denude, I was surprised to discover that Merriam-Webster's Eleventh Collegiate Dictionary doesn't provide a useful answer to the OP's question.
In its entry for denude, the Eleventh Collegiate gives the etymology as
But that dictionary's entry for de- is disappointingly incomplete:
The only definition here that is even remotely related to the OED's clear and succinct "down to the bottom, completely" definition of de- is the fourth one, which, besides being worded rather vaguely (in effect, "something derived from something else of a particular kind" as a noun and "being derived from something of a particular kind" as an adjective), doesn't offer an associated verb form with a definition along the lines of "derive from (something of a specified nature) [denominate]."
Merriam-Webster's treatment of de- appears to leave unexplained such common de- verbs in English as default, delimit, denote, denude, and despoil.
No, it should not.
You are assuming that the verb denude has been constructed from the adjective nude.
That is not the case. The latin root is dēnūdō (and hence present infinitive dēnūdāre, perfect active dēnūdāvī, supine dēnūdātum.)