How would I configure Pulse secure VPN for Windows to allow a user to connect to a Linux server ?
The easiest way is to use the Pulse Desktop Client. If your users deploy this then you only need to configure an ACL rule to allow access to the server. If you use split-tunneling, then you would also need a policy to specify the server as a resource that needs to be tunnelled.
Once the Pulse client is connected, then you can access the server with ftp, putty, or however you are used to accessing it without the VPN.
If you had something other than L3 VPN access, then please specify the use-case more specifically - that is to say, how do you want to connect, what do you need to do with the Linux server?