The best way is to format the card after you've downloaded all the pictures (and made sure they are on the computer (and preferably at least one backup device)). The format should be performed in the camera, not by the computer.
As you didn't specify the make and model of your camera, I can't tell you exactly how to do this, but it will be somewhere in the menu system. Some cameras also have a shortcut, usually involving holding down two buttons simultaneously.
Use a card reader plugged into a USB port. The computer will see it as another drive (or maybe more than that depending on how many types of card it will read) and you can then navigate to the picture files and delete the ones you don't want.
In camera, you select replay (right-pointing triangle) and you should get the option to delete each one.
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