The content type is part of an application feature

Recently I had the problem in a production environment that after the deactivation of a feature I was not able to delete the content types that I have generated within my feature from Site Collection.


Solution
But the solution is very easy. Following steps will help you to solve this problem:

1. You must find out all of usages of specific content type. I will suggest use SharePoint Manager 2010 and for every content type you will notice property called “Usages” it basically tells you where the content type is used. 
2. Then you can delete all of its reference.
3. Empty Site Collection  Recycle bin
4. Deactivate the feature
5. Your Content Type is now removed.

I hope i could help someone else with this post. Enjoy it :-)