You can use a loop and call dir
for each of the folders:
for %F in ("c:\Program Files\TrueCrypt" "c:\non folder\non subfolder") do (
dir /s /b /o:gn "%F"
) | findstr .sys
However, depending on what you need exactly you can probably do better by ditching dir
and findstr
here and opt for a loop over the files. But that depends a bit on what your overall goal is.