Gfilui

I am trying to save my configuration and data files to a usb before reinstalling 16.04 on same computer and reinstalling the the files to the reinstalled operating system.

Everything that belongs to the user is stored under

/home/<username>

In most cases configurations are "hidden", that means they have a dot . in front of them.

You can see them in a console with the command

ls -la

or you open your file manager in ubuntu go to your home folder and press

<CTRL>-h

this should show them.

If you get enough room on device, you may want to save all disk for safety before reinstall, or install on an empty partition, and then copy by parts to the new OS. An OS update keeps all user data and configurations, but if you choose to install the full OS, read about options and select wisely. Answering what you asked:
user data can be stored anywhere where write access is given, but most applications should default to user home ~ (typically /home/

configuration made by a user are in principle in the user home, in hidden files or directory, seen with:
ls -a ~

exemple:

.bashrc .config .eric6 .hplip .lesshst .ICEauthority .local .pki .thumbnails .xsession-errors.old
.adobe .dbus .gconf .profile .cache .dmrc .gimp-2.8 .ipynb_checkpoints .macromedia .python_history

.bash_history .compiz .gnome .ipython .ssh

.bash_logout .conda eric0.ini .gnupg .keras .mozilla .sudo_as_admin_successful .Xauthority

So saving all /home is a first step, then

Configuration made with sudo may be under /root under hidden directory,
or in many other places (/etc ...), but it is likely better to perform them again on a new clean OS, since the reason to reinstall maybe some misconfiguration you want to get rid of. Maybe you save as well /root and /etc and attempt to replace them after OS install without erasing, as:

sudo mv /root /root.ori /etc /etc.ori # rename the clean system dir
sudo cp /media/xx/root / # copy saved system dir 
sudo cp /media/xx/etc / # same

And try if this suits you. Any packages or applications that you installed, you must reinstall after OS reinstall