How can I convert some categories to a custom taxonomy?

I have a WordPress install that has a ton of categories. I want to convert some of these categories into a custom taxonomy. For example, I have:

Categories:

• Category A
  • Subcategory 1
  • Subcategory 2
• Category B
  • Subcategory 1
  • Subcategory 2
• Category C
  • Subcategory 1
  • Subcategory 2

And I would like to make Category C and all of its subcategories into a completely separate custom taxonomy. Is there a way that I can make this conversion, while keeping the relationships between Category C and existing posts intact?

You can create whatever new taxonomies you want to by adding register_taxonomy() function in functions.php

After that you can simply assign all the posts related to Category C to that custom taxonomy using Convert Post types plugin.