Malware Detected - How to Scan Via FTP

ipage said they found some infected malware, so they shutdown all my sites hosted with them and it's garbage. I don't think all of them are infected, i either have to delete every file they listed by hand or buy their service. Seems supspicious they're just trying to sell their damn sitelock service. A lot of the files they listed haven't been modified in over a year? I'm not sure how to do a scan via ftp, I tried googling and didn't come up with a whole lot. Is there an easier way to find the infected files? I would do an online scan but they locked all my sites and they're offline.