FTP stands for File Transfer Protocol. The idea is that it sets some rules on how to transfers arbitrary file formats from one computer to another. Flex3 website is a very broad definition, but, it's client would normally consist of HTML + SWF + some JS files. There should be no problem using those files with any FTP program. Judging from your question it seems like something didn't work for you, if I'm allowed to suggest: it is always better to tell the symptoms of the problem, rather then ask generic questions.
Best. Oleg
