You should use the postbuild task in your CSPROJ file (note that I only sign the "RELEASE" configuration):
<Target Name="SignOutput" AfterTargets="CoreCompile" Condition="'$(ConfigurationName)'=='Release'">
<PropertyGroup>
<TimestampServerUrl>http://timestamp.verisign.com/scripts/timestamp.dll</TimestampServerUrl>
<ApplicationDescription>my app</ApplicationDescription>
<SigningCertificateCriteria>/n "my company."</SigningCertificateCriteria>
</PropertyGroup>
<ItemGroup>
<SignableFiles Include="$(ProjectDir)obj\$(ConfigurationName)\$(TargetName)$(TargetExt)" />
</ItemGroup>
<Exec Condition=" '$(ConfigurationName)'=='Release'" Command=""c:\Program Files (x86)\Windows Kits\8.0\bin\x64\signtool.exe" sign $(SigningCertificateCriteria) /d "$(ApplicationDescription)" /t "$(TimestampServerUrl)" "%(SignableFiles.Identity)"" />
</Target>
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