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These are the two almos identicaly placed

Here you can see that there are actually two!

Yes, I know, OCD is pretty bad :P

And while you're at it, if you want as a bonus :p enter image description here There appear to be random faces inside the 3d object itself, or that's what I think by seeing those little dots inside the column, and not in the center of any face. how do you get rid of those?

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    $\begingroup$ I think Mesh>Vertices>remove doubles would work $\endgroup$ – moarorleslie May 15 '18 at 17:25
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    $\begingroup$ Remove doubles? $\endgroup$ – batFINGER May 15 '18 at 17:26
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In Edit Mode using "Vertex Select, Select the top left Vertex then while holding SHFT select the bottom left vertex press ALT+M > At Last.

enter image description here

Then do the same for the remaining two vertices. But as you can see from the drop down menu you can choose your own order to merge them.

enter image description here

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As mentioned in comments, multiple vertices that are in the same place can be removed by selecting them, and then pressing W while your cursor is over the 3d view area, and selecting 'Remove Doubles' from the pop-up menu. It is good practice to remove any doubled vertices that sometimes appear due to minor mistakes now and then, by selecting all vertices and doing the same thing.

The last part of your question is a separate matter (and thus preferably would be a separate question for better clarity, but no worries). From what you say, it sounds like this is one object, a column, with everything joined together. If so, you can select everything connected to it by selecting any part of it and then pressing Ctrl + L. Then, select the reverse of that by pressing Ctrl + I. That will leave selected everything that isn't part of the column. You can take a closer look at what it is by pressing . on the Numpad, which zooms to what's selected.

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