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://en.kioskea.net/download/download-11613-autorun-exterminator
Extract it --> Double-click on "AutorunExterminator" --> Plug your pendrive now.
This will remove the autorun.inf files from drives and plug your handy drive to
remove the autorun.inf file from it also.
Step 2:
Click on "Start" -->Run --> type cmd and click on OK.
Here I assume your drive letter as k:
Enter this command.
attrib -h -r -s /s /d k:\*.*
You can copy the above command --> Right-click in the Command Prompt and
paste it.
Note : Replace the letter g with your drive letter.
Now check for your files in drive.
Step 3:
After that, download the Malwarebytes' Anti-Malware from the below link
http://en.kioskea.net/download/download-105-malwarebytes-anti-malware
Update it --> Perform "Full Scan"
Note : Default selected option is "Quick Scan".
Good Luck.