Absolutely. Actually, Microsoft is in the process of deprecation of setup project template and obsolete Setup project type, which is not supported by MSBuild. What to do? I highly recommend Windows Installer XML toolset (WiX), which is fully wrapped for MSBuild and provides, among many other things, great integration with Visual Studio 2008 to 2012. This way, the complete project build from source code to the setup can be done both in Visual Studio and batch mode, from the same source solution.
This toolset is an open-source project, under CPL:
http://en.wikipedia.org/wiki/Common_Public_License[
^].
Please see:
http://en.wikipedia.org/wiki/WiX[
^],
http://wixtoolset.org/[
^].
See also:
http://en.wikipedia.org/wiki/MSBuild[
^],
http://msdn.microsoft.com/en-us/library/0k6kkbsd.aspx[
^].
—SA