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I'm trying to merge many flat surfaces (topology/map split up into areas) but the edge loops of all these surfaces are different and messy. How could I join them all into one flat surface - I'm not too fussed about the edges being exactly like one or the other.

If I use a Boolean Union, I end up with excess geometry (the final product has faces sticking out from where the original surfaces overlapped) and I don't know how to get rid of these. They aren't acceptable as I plan to extend the whole surface and 3D print the resulting volume.

using merge by distance and individually merging vertices takes too long.

Merging the edge loops also doesn't work because each surface has a different number of vertices around the edge.

Whole model underside of the model - there are no holes, just overlaps.

I'd appreciate any help I can get - I'm at a complete loss and can't do it manually because i'd be working for years.

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You may want to try the Weld modifier to a combined mesh.

Firstly, select all the meshes you want to "combine", and use the Object >> Join opertion so that they are all sub-parts of the same mesh object.

Then in edit mode get the edges/vertices that you want to combine with connecting surfaces. Here I used Select >> By Trait >> NonManifold to get the edges. You may not have to be too accurate although it appears that you are able to accomplish this from your screen-shot.

enter image description here

Now create a Vertex Group that you'll need to reference later. I renamed the VG from "Group" to "nonManifold":

enter image description here

Add a Weld modifier, specify the nonManifold Vertext Group that you created, and slowly increase the Distance (weld candidate vertices) until you are satisfied with the results:

enter image description here

In my example you can click the blue Mesh and Vertex symbols when in Edit mode to show before/after effects. Once you are satisfied, I'd probably Apply the modifier.

If you are left with some gaps you might be able to select these (Select >> By Trait >> NonManifold) and the "F" (Vertices: New edge/Face from from Vertices:

enter image description here

My example is trivial for a demonstration; you might have to create several vertex groups and weld each separately to avoid some blowups. That would reduce that value of doing it this way and again be too tedious.

Here's my example

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