The usual way is to use a colony of dermestid beetles to eat away the flesh. If you are near the seashore, I understand that marine isopods will do the same thing between one low tide and the next. You have to anchor the container for the skeleton very well to prevent the loss of bones.

I currently have this semi skelton frog . It still have muscles between bones which are hard to get rid of. I soaked it overnight with hydrogen peroxide but it did not remove all the flesh.