How to exclude Drive/vmdk or files from vmware virtual-based backup

You'd have to do this within the selection list itself. Exclude the *.vmdk from the backup, and then deselect the drive from the server.

Not sure on the 3rd option as it makes no sense.

Thanks!

Do not exclude at the VMDK level only do excludes at the whole VM level (you may have problems at restore time if you have excluded a VMDK within a multi vmdk VM.) Note if you have to eclude a volume from backups then it is recommended you revert back to traditional agent based backs and not use virtual agent backups. (which then unfortunately has a negative impact on the  simplicity of DR processes as a complete V restro is really easy from a VMware Agent backup but can be complex from a traditonal agent backup.

Also you might want to consider using includes only by deselecting at top level and then only selecting the complete VMs you need in each job. This will disable dynamic inclusion where the exclude method maintains dymanic inclusion. The reason for suggestion this is if your selections contain VM excludes mixed with VM includes it can be very confusing as to why a VM may not have backed up and looking at an include only list is therefore simpler.