The 3/18/13 episode of Bones titled "The Doom in the Gloom" begins basically with an incinerated body. 
These definitely provide forensic challenges.  The identification 
can't rely on a visual exam obviously.  Facial features are 
indistinguishable, tattoos are gone, and height and weight may 
be difficult to determine.  
Burn bodies are found in what is called a pugilistic attitude.  A 
pugilist is a boxer and when the extreme heat evaporates fluid from the 
muscles, they draw up the legs and arms.  The upper body position result
 looks like a boxer in their stance with arms drawn up.
Sometimes the heat is so intense the brain basically boils and 
explodes which causes skull fractures and damage.  An extensive 
examination is necessary to determine if the damage is done from the 
outside in (blunt force trauma) or from the inside out (heat related 
damage).
Going back to an identification of the fire victim, what to do if 
visual characteristics are not available?  If the fire is too intense 
then it is highly likely that the fingers are absent or badly damaged.  
Fingerprints therefore are not the option.
Nuclear DNA may not be an option either if the heat has damaged the tissues and muscles to such a degree that it has degraded.
Mitochondrial DNA may be the way to go as it is somewhat protected in the bone marrow or within the teeth.  
If the teeth are still intact then they will provide a good source 
for an identification.  Dental records for comparison are invaluable.
Medical records will provide a source for comparison in regards to 
prior surgeries which leave metal plates or screws in the body.  
Sometimes these can be traced through serial numbers.  So can most 
breast implants but they don't hold up well in a fire.
Previous broken bones or some indications of a disease or injury may also help lead to an identification.
Along side the identification accomplishment, the other challenges 
of retrieving evidence of what caused the fire, where it began, what may
 have accelerated it, and what items can be salvaged are also areas that
 keep the investigators busy in their job.

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