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Depending upon what your goal is, it's possible, though not advisable. In the early days of simple viruses, most remediation was performed manually, by removing the hidden and infected systems files, cleaning your registry, etc. Now, with the advent of advanced viruses, spyware and other malware, protected computing requires much more than just manual processes, as new code requires complicated removal routines.
But that doesn't mean you can rely solely on automated processes, and sometimes zero-day exploits require a level of hands-on involvement that hearkens back to those early days. There is the occasional exploit that could benefit from manual intervention, before the antivirus vendors have built a response, but the antivirus companies have shortened that time to such a small window that unless you're in the antivirus business yourself, the learning curve for manual removal is unusually not worth the effort.
Learn more about malware and its removal in our Antimalware Project Guide.
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