In fact the process of self-mummification was a very long and painful process that took 3000 days.
In the first 1000 days the monks would eat only local nuts and seeds which reduces their body weight severely.
In the second 1000 days the monks would only eat tree bark and roots which drained lots of water from their bodies. During the end of this phase they would drink poisonous tea made from urushi tree. It is assumed that the intent was to make their body too poisonous to be eaten by maggots.
The last phase is the actual mummification phase in which the monks will be locked in a crypt and meditate. Their only connection to the outer world was an air pipe and a bell which was rung every day.
The day the bell was not rung anymore, the pipe was removed and the crypt was sealed until the end of the last 1000 days.
Usually the bodies already started decaying by then, mummification was a mere exception which was seen as the proof that the monk has become a true Buddha and found their way to Nirvana. Though not being mummified the monks were honored and worshipped for their discipline and sacrifice.
Source: German Wikipedia entry about Sokushinbutsu
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Ouch
In-fuckin'-deed D-:
Edit: Just corrected some autocorrection mistakes. The part where " the monkey has become a true Buddha" made me giggle a bit. ;)