Hi,
There are a few options here, depending on your needs and the exact Unix environment. Here are some options that can hopefully get you started.
Option 1: Change the connection type
You may be able to set up a secure windows share (SMB) from the Unix server, that can be securely accessed like any other network share. If you tell me what flavor of UNIX you are using, I can point you in the right direction for that too.
Option 2: Connect using SSH components for .Net
There are a few SSH client components out there that you could use. Tamir Gal posted a great article on the subject:
sharpSsh - A Secure Shell (SSH) library for .NET[
^]
Hope that helps!