Answer Choice B & D has unauthorized use of had been,C is not correct for altering the meaning of the sentence or simply ambiguous enough.I eliminate answer Choice A for using "which" incorrectly .So the Correct answer is C
(A) a coat of filamentous structures was preserved with the fossil skeleton,
which are commonly recognized as the precursors of feathers.
(B) the fossil skeleton
had been preserved with a coat of filamentous structures, which are commonly recognized as the precursors of feathers.
(C) the fossil skeleton was preserved with a coat of filamentous structures commonly recognized as the precursors of feathers.
CORRECT(D) a coat of filamentous structures, which are commonly recognized as the precursors of feathers,
had been preserved with the fossil skeleton.
(E) a coat of filamentous structures
, commonly recognized as the precursors of feathers
, was preserved with the fossil skeleton.
Meaning error