Sometimes selection is easy. If for example duplicates are found in a different partition, then you can select using a rule on the drive letter, as explained in the aforementioned article. But what if the folder names are mixed and you can't come up with something robust to tell them apart? Then just tell the duplicate checker command to select them automatically for you (see picture). This automatic selection is good but has a couple of issues:
There is a way out of sorts. Although you must repeat the search, you can speed up the second pass checking only the duplicates already discovered — instead of your entire hard disk! So open up a new scrap container from Window menu, hit <Ctrl+A> to select all then drag-drop the duplicate files to the new window, and in there repeat the search for duplicates — and this time make sure you tick "Select all duplicates" in advance <g>.
The final gotcha: don't press <DEL> key to delete the selected duplicate files, use File > Delete menu command. You may remember that pressing <DEL> in all scrap container windows merely removes the items from the window, and doesn't delete anything.