As far as I can see, the Epson 3490 doesn't accept medium format negatives.
Unfortunately, very few scanners (either flat-bed or designated film scanners) accept medium format. Those which do are usually very expensive. See here:
http://www.theanswerbank.co.uk/Internet_and_Te chnology/Question188127.html
If you can get hold a suitable scanner, then the best software has to be Photoshop but, once again, this is pricey. For a good, free alternative, try Serif PhotoPlus 6.0:
http://www.freeserifsoftware.com/
Chris