Running the Malicious Software Removal Tool is easy.
The executable is self extracting. We double-click on it, and follow the prompts.

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The welcome page has a list of malware the tool detects and removes, so it's easy to double-check that the version we're running will remove Conficker.
Next we're prompted to choose a type of scan. For Conficker we want to pick the 2nd option: Full scan.

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Granted, on a file server with lots of storage, this could take a long time, but we've got to do it!
Next we see a typical progress screen, with a progress bar, and a list of what's currently being scanned, the number of files scanned, files infected, the start time and elapsed time.

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So, it's easy to know how much work has been done! If the MSRT finds an infection it will attempt to remove it.
Once complete with the full scan, the scan results are shown, we can view detailed results of the scan,

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and then click Finish.

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