Note: AVOIDING THE DEBATE ABOUT ANTIVIRUS !!!
Not all malware is a "virus" . For your user case, scanning a shared removable device, you can scan your flash drive from either Linux or Windows.
From Ubuntu see - How do I scan for viruses with ClamAV? .
Be warned, however, in general windows antivirus scanners are better if you still use windows.
Linux antivirus have 2 broad "problems" :
False positives - You will need to read and investigate the output of clamav and any reported "infected" files. Google search the reported file.
Linux antiviurs can quarantine suspect files, but there is no way to remove the virus from Linux other than to delete the files.
clamscan -r --move=/$USB/VIRUS /$USB
Where "$USB" is your mount point (see Why has Ubuntu moved the default mount points? )
Note: Linux security is very different than Windows security and in general "viruses" are almost non-existent in Linux.
Ubuntu security has it's foundations in :
Running with a limited account.
UPDATES - your system was patched long ago for all known Linux viruses. Updating is a critical feature of security.
I suggest you read https://wiki.ubuntu.com/BasicSecurity and https://help.ubuntu.com/lts/serverguide/security.html