Sony now has cd-players that support playback of ATRAC3plus (ATRAC being the minidisc compression format). So there should be a program, but I dunno if it encodes the files first, and then you burn it onto a CD, or if it encodes and burns at the same time. And then I don't think you'll have the ability to transfer the files anyway.
Also there are NetMD players. I dont' own one, so I can't tell you how it works. But it's suppose to allow for really fast transfers. Not sure about this, but I think the program takes sound files (i.e. mp3's) and encodes them, and then outputs through USB to the minidisc player. But even if it does this, I don't think you could use it for a non-NetMD player (or at least I haven't heard of any upgrade package that can make an existing MD player become NetMD).
What I've done is taken an older DVD player with optical output, and I just play CDs and hook it up to my MD player using optical. Unfortunately for me, my DVD player can't read CD-Rs and CD-RWs. I'd have to go to the family room to use the current DVD player to record from my own CDs then. Which really ain't that bad considering my family doesn't really sit down to watch movies all that often.