Go to the site JustUnfollow [dot] com and log into Twitter from there.
Use this iMacros script, set Play Loop to 50.
Code:
VERSION BUILD=7400919 RECORDER=FX
TAB T=1
URL GOTO=http://www.justunfollow.com/unfollow.html
WAIT SECONDS=0
CLICK X=411 Y=353
WAIT SECONDS=8
CLICK X=637 Y=311
WAIT SECONDS=4
CLICK X=113 Y=30
They say they allow 50 unfollows per day but I have done 100 at a time, but not on a daily basis.
They used to allow 100 unfollows per day, I don't know why they changed it to 50. Better safe than sorry I guess.
1000 unfollows may very well get your account shut down. Don't take the chance and ruin all the work you have done.