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When an anti-virus program "cleans" an infected program, it literally removes the virus/trojan from the program; there are many ways to do this, but for the simpliest explanation, let's just say it's not there anymore and it's not anywhere on the computer. The program that housed it (host) is, but the malware isn't. Now, this may render the host program incapable of running or doing anything, so it's best if you just delete it.
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