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I have run into imperfections with the mesh using the subdivision surfaces modifier before, but they were usually caused by either doubles or edges that penetrate the mesh. I tried removing doubles at a merge distance of 0.010, I tried degenerate dissolve and limited dissolve ruined my mesh. I also tried the recalculate outside method. I've looked around online, but other people's imperfections were caused by things I had already tried to solve, which weren't the causes of my mesh's imperfections.

How do I remove the imperfections near the eyes, including the creases and darker areas? enter image description here

So everyone can try things out and see if their solution solves the problem, here is a link to the file I'm using:

http://www.filedropper.com/ambiguoussave11

Thank you very much for any help. :)

Knowing your problems may one day be resolved, it fills you with determination.

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    $\begingroup$ To correctly remove them search the topic "face topology" and adjust your mesh accordingly. $\endgroup$ – Jaroslav Jerryno Novotny Oct 25 '16 at 13:21
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The imperfections in your model are mostly caused by faces with more than 4 sides (n-gons).
For an optimal subdivision surface calulation, you should try to use only 4-sided faces (quads). Triangles may look strange in some situations, but n-gons are smoothed pretty unpredictable.

You can find all n-gons in your mesh by selecting a quad, pressing Shift+G, choosing Polygon Sides and changing the Compare setting to Greater. Keep in mind that the first quad is still selected.

Faces selected after Shift+G You can see that these are exactly in the most problematic areas.

In order to create quads from n-gons, split them using the knife tool (K). You can combine triangles by pressing X and coosing Dissolve Edges.

I also added a few edge loops to get this result:

Wireframe after retopology

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before the "subdivision" modifier, try a "remesh" modifier (mode: smooth; octree: maybe 8; unselect remove disconnected faces). Then do a "decimate" modifier to a better/smaller poly count. Then do the "subdivision".

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