There's a good technology discussion (including the problems encountered
with decapsulation) on this issue at

http://spezia.eng.umd.edu/general/PEMs/pem1.html

Here's a procedure which was provided to me by Xilinx customer support for
decapsulating a BGA package (Amkor is a BGA package company).  This
encapsulant was especially tough - for other devices YMMV.  Different
devices may not need as much heat or different acids to successfully de-cap
them.  As always, observe all safety precautions!

***** from Xilinx *******
This is the procedure for decapsulating SBGA.  This was forwarded to us
by Amkor and I have tried it myself.  
 
 1. Heat your Hot Plate up around 210 to 250 deg.C
 2. Place the device to be decapped on the hot plate
 3. Drop 1 or 2 drops of H2SO4(98.08%) on the package using a Spode
 4. Reaction happens, then clean the bubbled surface with Acetone
 5. Repeat steps 3 & 4 until the surface of die is visible
 6. Drop 2 or 3 drops of Fuming Nitric Acid(92.0%) on the surface of
    the die and 1 drop of Surfuric Acid and then rinse them with
Acetone
 7. Repeat para 6 carefully until the area you want to see exposed
 8. Visual examination
**** end ********

-Gregg
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