Issues with notes in the wrong places

I've been using Anvil Studio for about a year now for my arrangements. I decided to switch to MuseScore so I could print them because I have someone that is interested in seeing some of my music. The issue is, Anvil will only save works as MIDI files. When I opened it in MuseScore, It was a mess. Everything sounded correct, but notes were literally all over the place, particularly in the piano and voice parts. Bass notes were in the treble, and treble notes were in the bass. The only way I've found to fix this is to completely rewrite or cut and paste the notes. Is there an easier way to do this? In Anvil, there was a feature that was literally called "move notes to other clef." That's all I need to do. Anyone know how? The handbook didn't say anything about it. If needed I can post a screen cap of what it looks like and what it's supposed to look like.