You can use aspnet_compiler for this:
C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_compiler -v /Virtual/Application/Path/Or/Path/In/IIS/Metabase -p C:\Path\To\Your\WebProject -f -errorstack C:\Where\To\Put\Compiled\Site
where "/Virtual/Application/Path/Or/Path/In/IIS/Metabase" is something like this: "/MyApp" or "/lm/w3svc2/1/root/"
Also there is a AspNetCompiler Task on MSDN, showing how to integrate aspnet_compiler with MSBuild:
<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Target Name="PrecompileWeb">
<AspNetCompiler
VirtualPath="/MyWebSite"
PhysicalPath="c:\inetpub\wwwroot\MyWebSite\"
TargetPath="c:\precompiledweb\MyWebSite\"
Force="true"
Debug="true"
/>
</Target>
</Project>