Thankyou Steks! I'll copy and paste the post from that forum that tells you how to remove perks.
random_noobie:
http://www.uesp.net/wiki/Skyrim:Skills
find the perk you want to remove/add.
use player.addperk and player.removeperk.
sometimes you need to exit the stats screen to update it.
So to remove Eagle Eye perk I opened the console (which is the ~ button) and typed player.removeperk 00058f61
When you remove a perk this way it doesn't give you back the perk point, so you will have to add perks using console commands for the ones you remove to keep the right number of perk points.