If what you mean is that you have all the document search results and want to clone them while retaining the (not shown) folder structure, you can use briefcases to do that. When you create a briefcase from search results, there's an option to retain the original folder structure. If you do that, and then re-import them, it'll retain the structure, metadata, etc. It's a bit of an extra step, but shouldn't be that huge a deal. That's the case where you don't have the actual folders present, as Wesley shows above. 

The briefcase option sounded promising but it did not work. I selected documents from a Search Result, then exported to a briefcase. I went into Options and selected the following: (see image)

When I went to import into another folder, it only imported the documents, it did not bring along the folders they resided in. 

I actually found another way around my issues, I will now just Tag the documents I need and run the workflow off the Tag instead of the Search folders/documents.