Does the pendrive appear empty (with full capacity free) under windows explorer? If so the files were erased, I've never tried a recovery software on a USB pendrive but I guess it's worth the shot, try Recuva.
However if it does appear to have content then it's very likely your files were hidden by a trojan/malware, how exactly did you run that command?
- First you need to run CMD with admin privileges (look for cmd in start menu, right click on it and choose "run as admin").
- Type the drive letter of your pendrive, i.e. F:\
- type in: attrib -s -h /s /d *.*