You can use screen. First install it with:
Then when you are using putty to connect to your server just type
sudo apt-get install screen
to open a new virtual terminal.
You can then start your minecraft server as usual. To detach from the virtual terminal hit CTRL+a and then d. This will detach the virtual terminal but keep all processes running in the background, you can then quit putty and Minecraft will keep running.
To recoonect simply open a new ssh session using putty and type:
to reconnect to the virtual terminal session.