Convert video files(.wmv or .avi) to flash movie file(.flv) using ASP .NET

I want to convert video files(.wmv and .avi) uploaded on my site to get converted to .flv. Searching the web I found ffmpeg(http://ffmpeg.mplayerhq.hu/) is a command line software which does the required conversion. But i don't know if it can be used with .NET. If it can be used then how..? If not then what is the other solution...?Can anyone help..? ...