Here is how I do it
<ItemGroup>
<BootstrapperFile Include=".NETFramework,Version=v4.0">
<ProductName>.NET Framework 3.5.SP1</ProductName>
</BootstrapperFile>
<BootstrapperFile Include="Microsoft.Windows.Installer.3.1">
<ProductName>Windows Installer 3.1</ProductName>
</BootstrapperFile>
</ItemGroup>
<Target Name="AfterBuild">
<GenerateBootstrapper ApplicationFile="Installer_x64.msi"
ApplicationName="Installer" BootstrapperItems="@(BootstrapperFile)"
ComponentsLocation="Relative" CopyComponents="True"
OutputPath="..\Output\AddIns\Installer_x64" Path="C:\Program Files
(x86)\Microsoft SDKs\Windows\v7.0A\Bootstrapper" />
<GenerateBootstrapper ApplicationFile="Installer_x86.msi"
ApplicationName="Installer" BootstrapperItems="@(BootstrapperFile)"
ComponentsLocation="Relative" CopyComponents="True"
OutputPath="..\Output\AddIns\\Installer_x86" Path="C:\Program Files
(x86)\Microsoft SDKs\Windows\v7.0A\Bootstrapper" />
</Target>
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