There's no such thing as "unix files" unix files are just streams of bytes, just like on most other operating systems (like windows).

The biggest difference is that windows distinguishes between text and binary files (it interprets the line-ending character differently for text files) while unix doesn't. See binmode and perlport.

If you want to read and write files from/to a unix machine, you can use all kinds of network protocols to send/recieve the files. Personally, I prefer to use plain scp to transfer files, since it's available everywhere, has good authentication mechanisms and is encrypted. There are also perl modules to do scp, but they tend to require a bit more work setting up, especially on windows. See for example putty for nice and free ssh & scp clients for windows.