Hi Ali, welcome to NST.
If you delete the boot folder, the system will no longer be able to boot !
It contains the BCD, which holds the information about the location and type of each of your systems.
To boot Ubuntu you must use EasyBCD 2.0 for any Ubuntu after 8.04. Make sure that you use the "advanced" button during Ubuntu install to prevent the default action of Grub replacing the Vista boot. Tell it to install grub to the Ubuntu partition boot sector.
In EasyBCD Go to "add/remove", click the Linux tab and select the partition where Ubuntu (and grub) is installed.
If Ubuntu is on the same HDD as Vista, that's all you need.
If Ubuntu is on a different HDD, you'll need to tick the "grub is not installed..." box, which will then cause Neogrub to be installed as a link to your Ubuntu disk.
EasyBCD is just a utility program installed on your OS. It's not the boot manager. It's not a part of the system. You can uninstall it at any time, just like any other app on your system using
Control Panel / Programs and Features / Uninstall.
Why do you want to format C\: ?
If you want to get rid of Vista and replace it with Ubuntu, that's got nothing to do with EasyBCD.
Just Install Ubuntu, and when it wants to know where, tell it to replace the entire HDD.
But be absolutely sure that's what you really want to do first
You paid a fair bit of the cost of your PC for the Vista software included. It would be wise to protect that investment by making OEM backup/recovery disks first in case you change your mind.
Why don't you tell us exactly what you're trying to do.
I'm reluctant to advise you with so little information about what you really want.