I think of naked as describing your whole body, or at least a very large part. But individual parts may be bare. "Bare shoulders" or "bare feet" both sound correct, but "naked shoulders" and "naked feet" sound very wrong. So to answer your specific question, I'd always say "bare feet" and never "naked feet".

Some uses of BARE are a synonym for NAKED Some uses of BARE are NOT a synonym for NAKED adjective 1. "he was bare from the waist up" synonyms: naked, nude (and others) 2. without addition; basic and simple. "he outlined the bare essentials of the story" synonyms: plain, essential, fundamental (and others) "the bare facts" only just sufficient. "a bare majority" surprisingly small in number or amount. "all you need to get started with this program is a bare 10K bytes of memory" synonyms: mere, no more than, simple (and others) verb 1. uncover (a part of the body or other thing) and expose it to view. "he bared his chest to show his scar" synonyms: uncover, strip, lay bare, undress, unclothe, denude, expose "he bared his arm"