I use the following for
Authenticode signing in my batch files:
SET SignToolMs="C:\Program Files (x86)\Microsoft SDKs\Windows\v7.1A\Bin\signtool.exe" sign /f %cd%"\MyProject\MyCertificate.pfx" /p myname
%SignToolMs% %cd%"\MyProject\bin\x86\Release\MyProgram.exe"
I first used
Dotfuscator for signing, but found this was not reliable.