It was perfectly normal for a body to be stripped and, in the case of a normal everyday death (rather than execution), be washed and laid out, and embalmed and sealed in a lead coffin if the family were wealthy. Poorer people would be put in a re-usable wooden coffin for the funeral and then be buried in just a sheet. In Anne's case, we know that she was stripped of her clothing, wrapped in white cloth and then placed in an elm chest before being buried in the Chapel of St Peter ad Vincula. She was buried as a traitor because she was executed as one. I'm sure that her ladies would have made sure that her body was treated with respect.
As far as her clothing is concerned, I would expect that any cloth that was not tainted with blood would have been re-used and the rest destroyed.