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Can I merge layers of same name in any auto script instead of selecting & merging one by one in pdf.

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    Yes, you can probably write a script to merge layers with the same name. – Luciano May 30 '18 at 13:54
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In this kind of problem, I would rather use prefix before each name. In example:

PREFIX_Folio Footer Slug.
PREFIX 2_Photo_Credits
PREFIX 3_Image_ID

Then, we could use an ExtendScript to make something like this:

var selectArr = [];
var test;
var layerName;

var layerArr = docRef.layers.everyItem().name;
var docRef = app.documents[0];

for (i = 0; i < layerArr.length; i++) {
test = layerArr[i].substr(0,5);

if (test == "PREFIX") {
     layerName = layerArr[i];
     selectArr.push(docRef.layers.item(layerName));
  }
}

var mergeLayer = selectArr.shift();
mergeLayer.merge(selectArr);

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