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I want to remove edges between two boolean-joined meshes as shown in the images below.

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  • $\begingroup$ One of the reasons to avoid boolean operations is that it creates irregular topology. It is always better to try to make your mesh as a single piece and keep the topology consistent (and quad based). Topology is your object, not a coat to be added on top. A common mistake is to create a highly detailed and subdivided object and try to grow it and add to it. It's easier to create a more basic object, that has the rough shape you need for the whole object, and from there you can start to subdivide it for finer detail. It will take you longer to fix this than it would take you to do it right. $\endgroup$ – cegaton Mar 23 at 21:59
  • $\begingroup$ Or if you have two different objects with the idea of joining them later, pay special attention to the the places where they should meet, so that they have the same number of vertices and that they are aligned. $\endgroup$ – cegaton Mar 23 at 22:16
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Honestly, I can only think of manually adjusting the verts to fit, or merge them. For merging verts, just select the edge loops on both parts, click on the merge icon on the bottom, and say S (scale) Z (locking z axis) 0. A way to use both methods, is to select a bottom vert on the top object, and the adjacent top vert on the bottom object, and say S, 0. Kinda tedious though.

Hope this helps.

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