You might want to check out the Elroy - Sparta trail, it's a nice trail with some really neat tunnels. Lots of little towns to stop in (the trail passes within a block of my folks house).
http://www.elroy-sparta-trail.com/
It's connected to the Great River and La Crosse River Trail to the west and the 400 trail to the south, so there's about 100 miles of rail trail within minutes of I-90.
If you've got time - I also recomend the Root River Trail in MN, it's beautiful.
http://www.rootrivertrail.org/



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