[bookfanmd]

Are you using Windows? If so copy them from the reader within the Windows explorer to a new directory. You should then be able to import them from that directory into Calibre using the second option on the Add Books menu (click the down arrow between the Add Books and Edit Metadata buttons). This will add from multiple directories (including subdirectories) assuming each file in a directory is a copy of the same book.

If the metadata files are still giving you trouble do a search within the Windows explorer of the new main directory for the .opf file type and then delete them from within the search window and try to import again. I didn't have any trouble re-adding my books back from the reader this way.