Hello,

If you did not format your flash drive, then 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 flash drive now.
This will remove the autorun.inf files from your flash drive and also from drives.
Step 2:
Click on "Start" -->Run --> type cmd and click on OK.
Here I assume your flash drive letter 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 : Don't forget to replace the letter g with your flash drive letter.
Now press "Enter".
Now check for your files in Flash 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.