Nintendo recently revealed amiibo support for Metroid Prime: Federation Force on Twitter.
Using either Samus or Zero Suit Samus amiibos will unlock both a custom paint job in the style of the character and special upgrades for your mech. Tapping any other amiibo will net you a cool custom paint job for your mech based off whatever amiibo you used. Mario and Bowser style mechs were shown off.
You can look at the images below. Metroid Prime: Federation Force comes out on 3DS August 19th for North America, and September 2nd in Europe.