Preparing an autopsy case can be much more challenging for an Embalmer than the standard case, however most are trained to handle such situations and are able to overcome the technical difficulties with excellent results. Many morgues in the United States make sure to preserve necessary vessels used in traditional embalming, just so that proper care can be given to the deceased and a comforting final image can be presented to the family.
There is usually no effect on final disposition, whether it is traditional burial or cremation.