How to prevent inside faces and non-looping edges when mirroring? I'm trying to create a model in Blender. It is symmetrical over the X and Y axes, so I used a mirror modifier over X and Y axis. However, when I apply the mirror, the edges don't "loop" and faces are created on the inside. This causes issues when UV unwrapping because on these edges seams are created even though I didn't mark them as seams.

I tried to prevent this from happening by turning off "clipping" in the mirror modifier and I've tried removing inside faces and non-manifolds.

https://imgur.com/a/PogTW


Model before applying mirror modifier.
The inside faces are probably due to the vertical edge at the far corner of your base model. Deleting that edge (and associated faces) should help. You don't need that geometry in your model, anyway.

For the surface vertices, did you try "remove doubles" with a sufficient margin to collapse the unwanted doubles, while keeping all others. It helps if your edge vertices are exactly on the XZ or YZ plane.