Every element has a counter to antimatter:
- phase dragons and immortals cannot be antimattered, quint can protect any other creature, fractal your creatures and opponent won't be able to antimatter all of them.
- eagle eye or shockwave to kill the antimattered creature
- kill the creature with drain life or just deny your opponent of quanta with devourers so that he is unable to play antimatter. Darkness works great with many little creatures (vampires, devourers), so it's quite effective against antimatter. Just be careful, because antimattered vampires damage you instead of healing.
- use aflatoxin or a virus to kill the antimattered creature, you'll gain skeletons and increase your bonewall in the process, vultures can grow back to positive strength after being antimattered
- burrowed creatures cannot be antimattered, you can burrow antimattered shriekers to halve their healing, you can also basilisk blood the antimattered creature to stop it from healing for 6 turns
- mutation, chaos seed... or use another antimatter to make your creature positive again
- firebolt your creature, cremate it, or wait until you can heavily damage your opponent with firebolts and only then play your creatures to finish him in one turn
- eat the antimattered creature with otyugh or use gravity pull on it
- you can usually play 6 cheap creatures before your opponent can play a single antimatter and some source of damage
- play flying morning glories, impossible to antimatter
- rewind the antimattered creature, play it once again and it will have a positive attack again, anubis can also be used to counter antimatter
- kill the creature with ice bolt or freeze/congeal it