You know, the one that outputs this=>
------ Clean started: Project: Foo.Bar, Configuration: Debug Any CPU ------
========== Clean: 1 succeeded,
Why not look for yourself? Open up Microsoft.Common.Targets (found under %windir%\Microsoft.NET) and you'll see a section like so:
BeforeClean;
CleanReferencedProjects;
UnmanagedUnregistration;
CoreClean;
CleanPublishFolder;
AfterClean
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.