Hi Andy, that is called "Z fighting" ( https://en.wikipedia.org/wiki/Z-fighting) and yes it's when you have duplicated objects occupying the exact same surface area.
The main way to avoid it is to remove or hide the duplicate copies if you don't need them for the immediate operation.
If you can post your .3dm model file that you show there and maybe describe a little more about what steps you need to do for the boolean that would make it easier to make some suggestions. It's hard to guess just from the screenshot alone why you are needing the duplicates.
Often times a more convenient way to keep an object around is to select it and use Ctrl+C to put it into the clipboard, then when you want to recover it use Ctrl+V to paste that in rather than keeping a set of duplicates around while working on stuff.
Sometimes using undo in combination with that can be good, like if you do a boolean and then see that you want to keep the whole cutting object around, you can use Ctrl+Z to undo the boolean, then select the cutting object and use Ctrl+C to copy it to the clipboard, then redo the boolean (I mean using Ctrl+Y Redo, the opposite of undo rather than actually running the boolean command again) then Ctrl+V to paste and that will then resurrect that older object into the current model again.
Also another thing that may be useful is you can use the Esc key to deselect objects as well as clicking on empty space.
- Michael
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