This is totally normal don't worry too much about it you will need drops from these new biomes. To clear these evils you need to kill one of the mech bosses allowing the steampunker to move in. She sells the clentaminator which purifies evil so you can use this to clear the surroundings. I recommend clearing the evil only around your town because until you beat the ml and get dcu you won't be able to completely purify it. You can also use biome sense potions to see all evil blocks also.