Ink eraser knife
In the nineteenth century, there used to be made a knife that was created especially for removing ink from parchment. It's blade was shaped like an aspen leaf, hollow-ground and exquisitely sharp. The shape of the blade in some ways imitates the shape of the lunellum, the knife which the klafmacher uses to thin and smooth the skin during processing and it is therefore extremely suitable for making erasures on parchment.
Unfortunately, they are no longer made, but they can still be found fairly easily on any number of sites specializing in old writing paraphernalia. They cost usually between 20 and 80 dollars or more, but are definitely a tool worth investing in. When sharpened properly, say to about the same degree of perfection as a knife used in shechita, these knives really are the very best thing for thoroughly removing stains and unwanted letters. They are much sturdier than a razor blade, or an X-acto knife, and give better results. They can also be resharpened.
When using this type of knife to erase, be sure to work lightly and in both directions holding the blade perpendicular to the klaf, never at an angle.