This shortcut virus you are talking about is infact a combination of trojan and worm, and is usually executed as shortcut.exe.
It consolidates every file in your portable devices and put it into one hidden folder. Then, it creates a Flash Disk shortcut.exe. Like the file and a folder shortcut virus, it will give you no choices but to click it to see your files. Once executed, it installs malicious applications that spy your computer.
Things to remember if you are infected by Shortcut Virus
1. Do not open your Flash Drive via autorun and from My Computer.
2. Open your Flash Drive and Hard Disk by right-clicking it, then click explore or type its drive letter in the windows address bar to prevent any script from running.
3. Unhide Files hidden by the virus, to see the real files which are hidden by shortcut virus and to avoid executing it.
Download these two tools, namely: Trojorm Removal Tool and Shortcut virus fixfolder (download this file and extract, put the extracted folder in infected pen drive)
Step 1: fixfolder.vbs (open this file from your infected pendrive, open in notepad and change your drive letter of pen drive)
Step 2: Trojorm Removal Tool v1.5.bat (run as admin after completing step 1.)
Download SmadAV Antivirus (Prevents viruses from infecting portable devices)
Download HFV Hidden Folder Virus (can disinfect and remove shortcut virus both from internal and portable devices)
Hope this works and do not forget to full scan your entire infected pen drives and computers even after removing this shortcut virus.