I wonder if they are galls of some kind... I think you might need to ask someone knowledgable, or post a picture. Where is the tree now - you can't leave it unpotted for any time at all or it'll just dry up and die.

Thanks Lucy, I went ahead and put it into a training pot in bonsai soil so it is OK. I had just never seen maple roots like that and the dirt it was in was unusual (dirt with a lot of clay). I just wondered if anyone had ever worked with these trees as bonsai. Zack