Firstly, shortcut virus is not a malware virus. You must therefore use a malware remover.
It is important to closely observe the virus. I take the pendrive case to explain the problem. Suppose you want a document to be copied from a public PC. When you plug this pendrive into your PC, you are amazed, shocked and dismayed (may be!) to see that all your files are gone and the drive has a special shortcut. The files were actually hidden.
The public PC or your PC might now be infected. If you're searching the files, then congratulations! Your PC is infected now. Every time you insert a flash drive, all files hide and create a simple shortcut to infect other systems with the shortcut. If you want your little kitten to be healthy, never open the shortcut.
There is a CMD command instead, which retrieves all the files in one go.
This process ensures that damaged files from windows are restored.