Is it safe to modify the figure part of an amiibo?

It is completely safe to modify your Amiibo, as the information that's stored is inside the base of the figure. (The NFC chip is actually a really thin wafer as seen on this picture):

Figure Image Found at this link: https://www.reddit.com/r/amiibo/comments/346ip6/is_it_possible_to_implant_an_amiibo_chip_into_my/cqsm204

From left to right:

• Figure (on top)
• Underside of base
• Cover of base
• NFC Chip (That's the part that's placed between the two)

The only thing to be careful of is using too much heat in modifying the base or near the base, as that heat can transfer and affect the NFC chip. (So if you use a glue gun on the base, give it time to cool between applications!)