When uploading documents into a document library with folders, you normally see the following screen:

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Problem 
On one of our sites the Destination Folder was not available. After some investigating I found that the site where it didn’t work, was created using the “Blank site” template. After some research I found a similar issue on the net.

Solution 
Since we used the “Blank site” template, some features do not get activated by default.

I found out that the feature that is responsible for the “Destination Folder” is the “Metadata Navigation and Filtering” feature.

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After activating the solution, the Destination Folder became available. Note that if you turn this feature off, existing libraries will be able to select a destination folder, as where newly created document libraries will not be able to use this feature.

More information

For more information about the Metadata Navigation and Filtering in SharePoint Server 2010, check this article.

Thanks for reading !!!
Happy Sharepointing