In a terminal use the next commands:

cd = Change Directory

cd /var/www

mkdir = Make Directory, this command requires elevated privileges, so run it with sudo or gksudo

sudo mkdir foldername

(where foldername is the name of the folder that you wish to create).

You can create subfolders from within /var/www without changing to the desired destination by using:

sudo mkdir foldername/subfolder

cp = Copy one or more files to another destination

cp PATHTOSOURCE/file.php PATHTODESTINATION

This can be used for any kind of file.

Note: If you wish to use a GUI for these tasks, you can use Nautilus with elevated privileges, simply hit Alt+F2 and write gksudo nautilus, then Enter after which you will see Nautilus File Browser, press Control+L and write /var/www and you can copy/paste or drag/drop anything you wish with ease.

For a comprehensive list of the commands, visit: http://ss64.com/bash/

Good luck!