Answer:
Alice is never naked in the book or Disney's 1951 animated film, Alice in Wonderland.
There is a story that in the 1951 Disney animation, there is a frame or two where Alice appears naked, but as far as VHS and DVD releases are concerned, this is completely untrue, and there is no evidence that it ever occurred in the prints of the film used when it was on general release either.
But she is naked in Tim Burton's 2010 movie, Alice in Wonderland. You can't see her however, because she is behind a bush.