MSBuild project file (*.vcxproj, *.csproj) is the .NET equivalent of Makefile.
Then what is the .NET equivalent of configure script?
You can pass the .sln into MSBuild with all the appropriate configurations. In MSBuild you can pass in which configuration you want at the command line.
Here is the list of command line options you can pass in: http://msdn.microsoft.com/en-us/library/vstudio/ms164311.aspx