while browsing through different blogs & forums, i have seen people are having hard time to unfriend unwanted people on Facebook, some users have reached their limits of 5000 friends,
easiest solution that i have found and tested is provided by getmyscript.com.
you can use their tool kit for facebook available in chrome store for free.

image credit @ technicalleaves.com

Steps to follow

1. Install Tool Kit for Facebook From This link.
2. Once extension is installed you will get an icon in top right corner
3. Open your facebook account & click on that icon.
4. Click on Removal Tools, and click on unfriend all Facebook friends, as shown in image belows
   

   How to unfriend everyone on facebook at once

5. after clicking this button your Facebook page will reload and unfriend tool will appear on top corner, as shown in image below.
   

   How to unfriend everyone on facebook at once

6. click on unfriend all friends , and few popups will appear asking you for confirmation, read carefully if there is any security check question answer it. if you did everything perfect the unfriend process should start and you will start to see following message on your screen.
   

   How to unfriend everyone on facebook at once

7. And you are done, in few minutes your friend list will be empty.