If you would like to have AVCHD file structure of just the select clips from each card you need to use Prelude. You could load the SD card into your computer, open in Prelude, pick your selects and ingest with the Transfer to New Destination option checked. This will build a new AVCHD copy of just your selects and maintain the AVCHD file structure wherever you choose to have it created.
I’d make a copy of the entire card as well as backup. But if you want to maintain the file structure and get rid of all the clips you don’t need then do it through Prelude.