In Visual Studio, what does the "Clean" command do?

The output directories - it removes the code that it's previously built.

It doesn't remove the bin/obj directories themselves (or the Debug/Release directories beneath them), just the actual .exe, .dll, etc files. Unfortunately this makes it less useful for my usual use of cleaning up output directories: when I want to zip up the source code. As the Clean action doesn't do this, I usually just delete the bin and obj directories directly.

Why not look for yourself? Open up Microsoft.Common.Targets (found under %windir%\Microsoft.NET) and you'll see a section like so:

<!--
============================================================
                                    Clean

Delete all intermediate and final build outputs.
============================================================
-->
<PropertyGroup>
    <CleanDependsOn>
        BeforeClean;
        CleanReferencedProjects;
        UnmanagedUnregistration;
        CoreClean;
        CleanPublishFolder;
        AfterClean
    </CleanDependsOn>
</PropertyGroup>
<Target
    Name="Clean"
    Condition=" '$(_InvalidConfigurationWarning)' != 'true' "
    DependsOnTargets="$(CleanDependsOn)" />

Keep reading to see exactly what each of those sub-targets does. (Some, of course, are just stubs for the user to override).

Personally, I like to see what shenanigans my fancy-pants IDE is up to behind my back. To this end, I'd recommend increasing the amount of info written to the Output window. Tools -> Options -> Projects & Solutions -> Build & Run -> MSBuild verbosity -> change from "Minimal" to "Normal" or "Detailed."

Try your Clean operation again and watch the output now! Correlating what you see to the *.targets files is a good way to start learning MSBuild.

It goes through your output directories and deletes any build related files in them.

I think you can also configure this by going to the Project's properties in

Configuration Properties -> General, under "Extensions to Delete on Clean"