Scanning Paper Animation w/ Registration?


I’m a senior animation student at LMU using Animate Pro 2 to help me create my film. However, I’m actually doing the rough and clean-up animation on paper, and then scanning it to the computer. I run it through Photoshop to strengthen the blacks and whites for better vectorization when I bring it into Animate.

The issue that I’ve run into is getting perfect registration. One of my professors told me that I could just scan it straight, and it would register. That worked once, but not with another scene. Since then I’ve tried marker over the registration holes so that I can at least use that to help me manually align it. I’ve heard that using black tape on the back and clear tape on the front will do the trick, but I haven’t had a chance to try yet due to time constraints.

You can see the trailer for my film here:
The lines are clearly jittering, and I’d like to find the best way to eliminate that.

I was wondering what I should try next? Or if there’s some step that I’m missing to tell Animate Pro to register it, rather than just importing the files and expecting them to be auto-aligned?