I assume you're trying to do this in AHK?
you need 2 nested loops, something like this
pub = MM,MC,FE,CS,RE,VL,WR
loop, parse, pub, CSV
{
Loop, %a_loopfield%_%date%_*.pdf
Runwait %comspec% /c pdftk %filename1% %A_LoopFileName% cat output MTR_%date%.pdf
}