Insert this line in the top directive region of your autoit code. For example, here is what we have in the ACC_Toolbar_Buttons.au3
#Region ;**** Directives created by AutoIt3Wrapper_GUI ****
#AutoIt3Wrapper_Icon=AEG-logo.ico
#AutoIt3Wrapper_Res_Fileversion=5.0.0.0
#AutoIt3Wrapper_Run_AU3Check=n
#AutoIt3Wrapper_Run_After=""cert_signer\Cert_Signer.exe" "%out%" /NoPopup"
#AutoIt3Wrapper_Tidy_Stop_OnError=n
#EndRegion ;**** Directives created by AutoIt3Wrapper_GUI ****
Command line, like this - C:\Users\l738606\workspace\Toolbar Buttons SQL\cert_signer>sign_file.cmd “<path and exe filename>” keys\AEG_App_Cert_cert.pfx Toolbar2012 . Note that Toolbar2012 is the password required to use the certificate to sign the executable.