SSH would probably be what you are looking for.
ssh is built into Linux
scp can be used to copy files from one computer to another via the command line.
man ssh
man scp
ssh some.hostname.here
or
ssh <ip.add.re.ss>
You can download
putty and pscp to access your Linux box via ssh from a windows machine.
you can download
winscp for a GUI interface you can install on Windows to copy files to and from your Linux box