Yes. As far as Windows is concerned it is just another drive. However, you will need to ensure that it always has the same drive letter (or letters) every time you connect it.
Windows gives new drives a letter in the order in which they are attached, so if you set up the external drive and it appeared as, say, E: and the next time you connected a card reader first, the card reader would be E: and the external drive would become F:. In that case, your programs probably would not run.
Some programs will run if they make no entries in the registry.