If you are asking about security while the file is being transmitted across a network or the Internet - the simple answer is scp (secure copy). The remote server (the one you are not directly logged into) must be running the ssh (secure shell) server (this is quite common). A google search will show you the syntax for ssh. This process will encrypt the data and the user name and password which you use to connect to the remote server. If you have a lot of files to copy or need to do the process by a scheduled task this might be the best bet.
There is a nice GUI client for Windows called Winscp. There are no doubt some for Linux/Unix as well although I have not used one.
Another idea... If you are using Gnome as your desktop you can create a launcher (shortcut) to the remote server using ssh. I have several to connect between my servers. The location is specified like
When I click on the launcher it opens a Nautilus window pointing to my server called "taylor10". I can simply drag and drop files to or from the remote server. Note that I did save the remote server ssh key, user name and password when I first created the launcher and I do not have to deal with these each time. Otherwise it will prompt for the user name and password each time it is launched.
You can also do this with the KDE desktop.