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So, I used a Boolean modifier on Suzanne and a fairly default cylinder. The results, as they move along, go something like this: video.

The modifier is set to union. As you can see, something strange is happening: only her eyes appear. I did do some interesting things with it previously using the subsurface modifier - but that time, her eyes dissapeared, as opposed to the rest of her head!

Kudos to anyone who can help me with this.

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    $\begingroup$ The eyes are not connected to the default Suzanne, resulting in a non-manifold mesh. This makes things tricky for boolean operations. $\endgroup$ – gandalf3 Dec 16 '14 at 2:30
  • $\begingroup$ Hmm... how did I make it so only her eyes dissapeared? $\endgroup$ – user1833028 Dec 16 '14 at 3:06
  • $\begingroup$ Well, it results in kind of undefined behavior. So it's unpredictable. $\endgroup$ – gandalf3 Dec 16 '14 at 3:15
  • $\begingroup$ Edit Mode - Select non-Manifold - F, then it works well with booleans. $\endgroup$ – user9528 Dec 16 '14 at 11:55
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You are using a non manifold mesh. Basicly, non manifold means, in layman's terms, not water tight.

Here is an example:

enter image description here

The cube has a hole in it. In Suzanne's case, its the fact that her eyes aren't attached to her head.

Here is a quick way to fix Suzanne:

enter image description here

Note: I use the loop tools add-on accessed by W

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    $\begingroup$ Note that blender has a bridge tool built in which AFAIK can do everything the loop tools version can. $\endgroup$ – gandalf3 Dec 16 '14 at 11:57

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