Well, we need to know a little bit about your server and the nature of the problem first.
What OS is your server running? If Linux, do you have access to a command line shell? Also, what kind of files are they and where (ie. in /tmp or your home directory)? If Linux, run the command "file (path of file)" and post what kind of file it is and also give the name of the file. You might try uploading the suspicious files to http://www.virustotal.com
The Hacked Site Recovery page was just updated recently and has some pertinent information to get you started.