Cutting of two aligned meshes at the same time

[mattherrmann95]

I want to compare two meshes, but cut out a little part of both of them.
After aligning the two meshes, there is a small part of one of the meshes which sticks out.
So what I want to do is aligning the two meshes, cutting a part out (for both meshes at the same time, so that there is no part sticking out on that specific part of the mesh and they have the same edge/surface on one side) and compare the rest of the mesh which is left after the cutting (Hausdorff distance, RMSE).
Is that possible? I couldn´t find any solution anywhere else

thank you!