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I planted 26 emerald arborvitae trees this summer. All but three are looking good. On each of those three, one of the shoots died. If I cut that part out, will the trees fill in?

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Yes, it will if those cedars are healthy. You should investigate to find out why the shoots died. Some possible causes with freshly planted cedars are:

  • inadequate watering; new plants need a lot of water the first season
  • too much watering: are they planted in a very wet area?
  • spider mites or scale or leaf miner are common problems. See here
  • physical damage during planting, deer

These answers are also related:

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  • 2
    Also check 'verticillium wilt'...
    – stormy
    Sep 24, 2015 at 22:19
  • Also if a branch has no green, it will die.
    – nportelli
    Oct 15, 2015 at 18:12

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