I have created backup copies of my main account private key file in a USB and also saved it in other laptops. I want to remove this main account from my Mist Ethereum Wallet. Is it safe to do this? I don't want to loose all my funds. :)
It should be safe as long as you have backups.
Best to test it out:
Move your main account private key file into another location.
Run Ethereum Wallet. Your account should have disappeared.
Move your main account private key file back to the original location.
Run Ethereum Wallet. Your account should have re-appeared.
If your results are as expected, it should be safe to delete your private key file, since you have the ability to restore your private key file correctly.