How to filter to be signed files?

I'm using windows-installer to pacakge my applciation and sign the executables. But there are thousands of executables in the application, and most of them are not needed to be sign, but widnows-installer will sign all of them by launching signtool.exe one by one, it takes too much time (more than 10 minutes) for packaging.
In fact, there are less than 10 files need to be signed, are there any methods to filter the to be signed files? Exactly, I don't want to launch signtool.exe so many times.