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According to some valuable feedbacks I modified my answer:

The Same Problem:

I had more than one Calibre libraries since I have imported the e-books' folders from my computer as libraries. I wanted to combine those libraries as one (merge) but I wanted to maintain the folders' hierarchy or at least I wanted to organize and see the e-books as if they are in the corresponding folders.

My Solution:

Create an empty library. Name it anything but this will be the one and only your Calibre Library. Of course you can rename it in Calibre later.
Create a custom column from "Preferences
-> Add your own columns -> Add custom column -> Comma separated text, like tags, shown in the tag browser" by adding lookup name and column heading. Column heading will be used to enter the name of the merging library (that is your folder name).
Copy your e-books in the existing library to the one created in 1. Let's call it main library or anything you want.
Without copying other library, select all the e-books and edit metadata. In the "edit metadata" window you will see a second tab "custom metadata" where your lookup name appears. Fill the blank as the corresponding library name (that is your folder name).
Now on the Calibre left column you will see your custom column and its subgroup as your added library (that is actually your exported folder name exported as library).
Repeat the same process for other libraries from number 3 to number 5.
You will now have your special column and all the different libraries as subgroups. You will have one Calibre library with different subgroups. This is powerful than using tags for this purpose since subgroups are your choice of organizing your e-books.
Since I had many Calibre library, I tried to merge them copying one by one. You may have many folders of e-books each organized in your way. You can add your e-books one folder by one folder using the process explained from 3 to 5.
At the end, you will have one Calibre library with different subgroups on the left panel. Subgroups will be anything you want, for example your e-books' folder hierarchy in your PC or Mac.

The original answer was:
"I wanted the same. I preferred the following solution; manual.calibre-ebook.com/sub_groups.html


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