How did Baxter Stockman remove his own brain and put in a robot body?
 

Well, how did he do it? Once it's disconnected from the hands, well...

interesting question.
maybe it was from the Triceraton technologies and the foot mechs that had been developed

he did it very carefully.

To be clear, we're talking about Mirage Vol. 2?

Yes, that's the only instance I know of when he actually removed his own brain. The only other version of Baxter to be a disembodied brain is the 4Kids version, and he didn't do it by himself or even voluntarily.

Punishment by Shredder
 

Baxter was subjected to harsh punishments by the Shredder on more than one occasion.

I figure he programmed the robot to do the surgery, with its fine motor skills and razor claws or something.

After all, he's gotta rely on something to hook him up; he can't do it himself.

But in the 2003 it was my servant and second in command Hun who kidnaped him then ordered foot techicians to remove it through surgery and connect it to a machine on jar as punishment for attacking me on TCRI.We didnt put him into a robot because we knew how dangerous he will be so we had just on jar where he couldnt do anything else than talking. How could i knew then that chaplin will put him in a robot while i was not there.... If i knew i woulldnt allow it.