I'm a novice Blender user and I could use some advice on cleaning up some unintended mesh.

I'm working on a 3D model that I extracted from microscopy data. For this purpose the volumes are extracted from the raw data using a program called AVIZO. Then I exported the volumes to blender for smoothing and animation etc. I've been working on the model for a couple of months and I was adding the finishing touches when I found out that there was a lot of unintended mesh inside of the model. I think that I must have been sloppy with the "fill holes" or "fill" functions in an earlier version of the model.

I've deleted part of the unintended mesh by hand but it takes a lot of time. I'm wondering if you know a faster way of cleaning it up? Due to the pending deadline I don't have enough time to go back to an earlier version. I can provide some screenshots of the mesh if that helps.

I hope it's okay for me to ask such a question on this forum.



This is the screenshot of my mesh. As you can see there is a lot of stuff going on in the centerpart.

enter image description here Edit:

I've uploaded the most troublesome part of the mesh

  • $\begingroup$ Yes, a screenshot would help. I assume that those unintended faces are connected to the "hull" mesh? $\endgroup$
    – morph3us
    Dec 20, 2018 at 11:01
  • $\begingroup$ Hi, could you provide the blend file to take a look? $\endgroup$ Dec 20, 2018 at 13:46
  • $\begingroup$ Hi @morph3us, Sorry for the late reply, another project came up and I haven't had the time to look at this again. I've added a screenshot now. Any idea how I can fix this more easily? I've removed part of it by hand but I do actually need the shapes as the originally were... $\endgroup$
    – TanukiTime
    Jan 16, 2019 at 10:28
  • $\begingroup$ In Edit mode use "Select All By Trait" from the "Select" menu and try "Interior Faces" and "Non Manifold". $\endgroup$
    – rob
    Jan 16, 2019 at 10:37
  • $\begingroup$ @rob, I tried both but it didn't really work $\endgroup$
    – TanukiTime
    Jan 17, 2019 at 11:38

1 Answer 1


Your mesh is really a mess.

I think the method I show here can help you with it.

In Edit mode, wireframe view, use the border select to select the up and bottom parts.

Hide them or invert the selection.

In case you use HIDE: Select all the rest and separate it (do not delete it because you can need it later ).

Now the interior is a separated mesh.

See the image below.

enter image description here

  • $\begingroup$ Hi, thank you for the instructions. Sadly.. it's the top and bottom that I need, the inside is the result of using the "fill holes" function without proper overview of what was happening. I should've clarified that, sorry! $\endgroup$
    – TanukiTime
    Jan 28, 2019 at 12:39
  • $\begingroup$ Hey, I accidentally downvoted your answer a few hours ago and didn't notice. I can't seem to change my vote now. Your answer is alright, please disregard the downvote. $\endgroup$
    – Najm Hoda
    Jul 17, 2020 at 19:34

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