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In Blender 3.2 - I have created 10 cubes using an array modifier having a relative offset the same as the side of the cube. After I apply the array modifier; when I select its faces, I don't see any overlapping vertices, but the checker deselect doesn't work, it only deselected the active cell. The object seems to work as an array of separate objects rather than 1 object. Do you know how to fix it?

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I have tried to separate by loose parts and join again, but it did not help.

When I do the same using an object created through repeating face extrude, the checker deselect works as expected.

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    $\begingroup$ Just to be sure.. was 'Merge' checked in the Array modifier? $\endgroup$ Jun 26 at 19:41
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    $\begingroup$ @moonboots Vaasha seems to be having this problem after applying the modifier, the way I read this... I can't reproduce ,,, $\endgroup$ Jun 26 at 20:12
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    $\begingroup$ oops ok........... yes yu must be right about the merge option $\endgroup$
    – moonboots
    Jun 26 at 20:15

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Checker deselect only work on contiguous selection.

Make sure all the faces are connected by using the Merge (Alt+M) -> By Distance tool

Then the checker deselect should work.

You can avoid this step in the future by enabling 'merge' on the array modifier like the comments pointed out

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