I know it is possible to do it via "root". But how about a reseller access?Who is your hoster?
Your host should be able to do this for you fairly easily and a lot quicker
than you can do for yourself as a reseller.
If you want to do it yourself, you will need to go into the control panels
for each customer (assuming you are using WHM / Cpanel) and generate
a "cpmove" (full backup) for each account.
If your host has backup services turned on, the accounts may already
have a backup held somewhere. Again, that is a question for your host.