Can Automise 2 be used for SFTP? If not can anyone recomend an alternative tool. Thanks in advance.
not yet, but we’re working on it 
I would recommend you have a look at cURL, it looks like a pretty complete utility for SFTP and heaps of other stuff and has a good command line interface:
Homepage: http://curl.haxx.se/
Manual: http://curl.haxx.se/docs/manual.html
"curl is a command line tool for transferring files with URL syntax, supporting FTP, FTPS, HTTP, HTTPS, SCP, SFTP, TFTP, TELNET, DICT, LDAP, LDAPS and FILE. curl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, kerberos...), file transfer resume, proxy tunneling and a busload of other useful tricks."