English Translation
Please make yourself comfortable.
What is “es” doing in this sentence?
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Good question, next question. 
It somewhat literally means “Please make it comfortable to you(rself).”
Most people probably won’t think too much about this, but I think the “it” might refer to the place where you are, or the environment. You may want to rearrange some pillows, or move a chair or something. You basically transform the place into something that’s comfortable to you.
The other common sentence one might hear is similar in English, but different in German:
Please make yourself at home. - Bitte fühlen Sie sich wie zuhause.
The German means “Please feel like you are at home”. Here, you are basically asked - or given permission - not to be shy about rearranging stuff to suit your needs. So it’s slightly different, but the effect is the same.
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