Check whether the files are not in hidden mode. Follow the following steps.
Step 1: Click on the below link and download the file "AutorunExterminator" http://ccm.net/download/download-11613-autorun-exterminator
Extract it --> Double-click on "AutorunExterminator" --> Plug your External hard drive now.
This will remove the autorun.inf files from your External hard drive and also from the drives.
Click on "Start" -->Run --> type cmd and click on OK. Here I assume your External hard drive as G:
Enter this command.
attrib -h -r -s /s /d g:\*.*
You can copy the above command --> Right-click in the Command Prompt and paste it.
Note : Replace the letter g with your External hard drive letter.
Now check for your files in External Drive.
Step 3:After that, download the Malwarebytes' Anti-Malware from the below link
Update it --> Perform "Full Scan"
Note : Default selected option is "Quick Scan".