I'm new to clamwin antivirus. I have this removable storage that was infected. The infected file was hidden and can only be seen when I unchecked "Hide protected operating system files" in folder option. I tried to full scan the storage but it did not detect any viruses but when I scanned with other antivirus it detected something.

Can clamwin detect viruses that uses rootkit?

it would help if you were a bit more specific than "detected something". You can always scan a file online at https://www.virustotal.com and see what different AV vendors detect

As Alch said, you need to be more specific. There are several rootkit viruses around, and some antivirus programs are not set up to detect them or will only detect a few. ClamWin uses the Clam signature database. A search of the ativirus signature database at the ClamAV web site using the term "rootkit" turned up one name: Trojan.Rootkit-6. This is Clam's name for it--other antivirus software will have their own name for it. There are some free rootkit removal tools available on the Web--especially for the Sony Rootkit.

Regards,

use this tool https://www.microsoft.com/technet/sysinternals/utilities/RootkitRevealer.mspx https://www.microsoft.com/technet/sysinternals/utilities/RootkitRevealer.mspx

and look for files hidden to the api
please note you can get false positives if you are doing something in background
so temp file and internet cache can be ignored
you need to focus on .sys or .dll that are hidden to api
often you have a .sys driver that starts and hides the malware executable.
I was happy to notice that clamwin can detect some of rookit hidden files
because of using unc paths