How to properly recover data from "broken" hard drive?

Hello Mac users,
I have a mid 2012 Mountain Lion MacBook Pro. My hard drive recently failed. As I have been working in Thailand, I decided to bring my laptop an Authorized Service Provider (Macintosh Center Co., Ltd.) in Bangkok. Their diagnostic was that my hard drive wasnt working anymore, and I had to change it. The problem is, since I had no backup, I asked them to recover my data and transfer to the new hard drive. But, this Apple Authorized Service Provider told me I had to go somewherelse because they have no software to recover my data! So, I went to the local Joe's repair computer store who retrieved my data from the problematic hard drive to the new one. Now, the problem is that all my "old" data is located in "orphan folders". In other words, counteless files were retrieved without folders and settings.
So, I would like to know if it is possible to recover my data with all the settings I had and then transfer it to my new hard drive. If it's possible, what software should I use to properly recover my data? If it's not possible, how should I deal with the "orphan folders" and my current settings?
Thanks in advance for your help.

First stop using your system, then get a copy of a program that will recover files like Data Rescue 3.  If you have a time machine backup you may be able to restore them. 

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