frustrating, isn't it? that has a bit to do with the triangles of the mesh. if the triangles aren't as condensed then you'll get more jagged cuts. There are more powerful softwares that can straighten it out the edges to be smooth - but it's been a while since i've done that so maybe somebody else could chime in on how.
I think you can also take the mesh into a different sofware, condense the triangles - then you get a bit cleaner cut that way
I'm assuming you're referring to exocad and editing a mesh? If that's not correct, then disregard this info. Rather than closing your selection in the edit mesh step, leave it highlighted and hit "delete" on your keyboard, it will cut the mesh straight rather than follow the stl triangles.