Hi Joe,
Use a good anti virus which is up to date. The issue which u were facing is due to virus on your local machine. use anti virus virus like bitdefender total security, kaspersky to scan your machines. keep in mind that your virus scanner is up to date. scan all the areas of your machine the finally plug your thumb drive and scan it too. After clearing all the virus, thread, warm, syware in your machine. then you can easily format your pen drive. And you can also see the disks pace is full free of total size.